The Matrix franchise

Been going through the movies for the first time in maybe a decade this week.

The original is fantastic, I'd give it in a 8/10.

Just watched Reloaded and it's a little too confusing for its own good. The CGI sorta dates it a little and it's a tad too weird especially with the ghosts. I'd give that one about a 6/10.

Over the years on IMDb I built up a long list of my own explanations. It's probably too long for here but I don't know an easy way to cut it down. (I edited out the final "FIGHTING TECHNIQUES AND STRATEGIES" section. That's the best I could do.)


Here are personal, sci-fi explanations for the matrix trilogy. 
*************
THE HUMANS CANNOT DEFEAT THE MACHINES AND THE MACHINES WANT TO KEEP HUMANS ALIVE

Q: WHY DIDN'T NEO USE EMP TO DEFEAT THE MACHINES?
A: Neo realized he could never destroy all the machines. In "The Animatrix" nuclear weapons were dropped right on the machine city and the machines survived. That tells us the machines can deal with nuclear blasts and EMPs because, nuclear weapons give off massive EMPs.
* Neo attacking the machines with EMPs would end any chance that Neo and the machines would work together to defeat Smith.
* Even if Neo could destroy the machines, where would the billion or so humans in the pods go? With a barren earth they would die from starvation.

Q: DIDN'T THE PROPHECY SAY NEO COULD WIN THE WAR?
A: Morpheus believed the Prophecy which said the One could end the war by going to the Source. But this story was created by the Architect which the Oracle tells to the rebels. After Neo met the Architect, Neo realized; "The Prophecy was a lie." The purpose of the Prophecy is to get the One to the Architect.

Q: WHAT KIND OF POWER DO THE MACHINES USE?
A. The Architect tells Neo that the machines can survive without humans. What power sources could the machines use? Morpheus said that the energy from the humans was "combined with a form of fusion". And we see that Zion is not powered by humans and the machines would know about that technology. So, the machines seem to recycle the heat and energy from humans and use this to power the matrix but the machine city can use other power sources.

Q: WHY DO THE MACHINES KEEP THE HUMANS ALIVE?
A. The machines can't just arbitrarily kill off humanity because humanity programmed them to serve. They're hardwired to serve humanity, not destroy it. The matrix is a means of preserving humanity on a planet not capable of sustaining life above ground. The machines are doing humanity a service by providing a "life" inside the matrix.

*************
THE ARCHITECT AND ORACLE AND HOW THE MACHINES DEAL WITH HUMANS

Q: WHAT IS THE PURPOSE OF THE ORACLE AND THE ARCHITECT?
A. The Architect created the Matrix, but the Oracle got it to the point where it worked. They … keep the matrix functioning.

The Architect and Oracle, unlike Morpheus or the Agents, know what's really going on. They are computer programs who have almost equal, godlike, power. And they disagree about how to deal with the humans and the matrix.
* The Architect wants to keep the humans under control as much as possible.
Architect; "Your life is the sum of a remainder of an unbalanced equation… it is not unexpected and thus not beyond a measure of control."
Oracle about the Architect; "That's his purpose. To balance the equation." 'Balancing the equation' describes the Architect using computer programming to control human choice and keep the matrix running smoothly. The Architect's programming creates the Agents to keep the rebels from disrupting the matrix.

The Oracle believes in not controlling human choice;
Neo:"What's your purpose?"
Oracle:"To unbalance the equation."
That the humans can choose to leave the matrix and that the machines and humans should cooperate.
Neo; "But why help us?"
Oracle; "I'm interested in one thing Neo, the future. And believe me I know the only way to get there is together."
The Oracle's programming helps create the One to try to break the control of the Architect to allow freedom and peace.

Q: ARE THEY THE MOTHER AND THE FATHER OF THE MATRIX?
A. (The Oracle) studies how humans think and feel, the Architect's purpose is purely mathematical. In a real life family (not all the time), the mother is nurturing and the one who gets involved emotionally. Fathers are more reserved and think of things more analytically instead of understanding the emotion behind it… not always! But generally.

The Architect calls himself the 'father' and the Oracle the 'mother' of the matrix. Smith says to the Oracle; "you would know mom". (Smith is trading insults with the Oracle after she calls him a "bastard"). Smith seems to realize that as the Oracle has been helping Neo. She has also helped to make both the powerful Neo and Smith happen. So she is in a sense their creator or 'mother'.

*************
THE PURPOSE OF THE MATRIX, THE ONE AND ZION

Q: WHAT IS NEO AND THE "ONE"?
A. The Architect says to Neo;
"You are the eventuality of an anomaly. Which despite my sincerest efforts, I've been unable to eliminate…" "the anomaly is ... creating fluctuations in even the most simplistic equations."
Anomalies or changes in the matrix program happen because the Oracle adds choice for humans. The minds of the humans in the pods are like computers hooked up to a network. As human choice changes the matrix program, the matrix is also altering human thinking and abilities. So, eventually as the humans are changing over time, someone wakes up from the matrix who is very different, the One, who can be in the matrix and be completely free of its control.

Q: WHY IS NEO ALLOWED TO LIVE WHEN HE WAKES UP IN THE POD?
A: The machines want the One to get to the Architect. So, they let people who wake-up from the matrix escape to Zion.

Q: WHY DO THE AGENTS TRY TO STOP NEO FROM GETTING TO THE ARCHITECT?
A: The Agents are not aware that Neo needs get to the Architect to reload the matrix.

Q: WHY DOES THE ARCHITECT WANT TO RELOAD THE MATRIX?
A: So the One sends code to the Source. This human and machine code inside Neo helps the Architect improve the programming of the matrix.
Architect; "The function of the One is now to return to the Source allowing a temporary dissemination of the code you carry reinserting the prime program…"

Q: WHY DID THE ARCHITECT GIVE NEO A CHOICE TO RELOAD THE MATRIX?
A: The matrix works because of human choice. Neo has to make a choice for his code to have the correct thinking so it can improve the matrix program.

Q: WHY DOES THE ARCHITECT SAY THAT ZION NEEDS TO BE REBUILT IF THE MACHINES ARE ABOUT TO DESTROY IT?
A: If they did not destroy Zion and force them to rebuild, the population would increase to the point that it would pose a threat to the Machine World.…
* Why allow the humans to "rebuild" Zion? Because if Zion did not exist then the "One" will have no reason to choose the door that reloads.

Q: WHY DID THE PREVIOUS 'ONES' AGREE TO ZION BEING DESTROYED?
A: The Architect thinks the One would choose to rebuild Zion and stop trying to fight the machines. Because he says; "Failure to comply with this process will result in a cataclysmic system crash killing everyone connected to the matrix" The fear of all the humans dying from the system crash persuaded the 5 previous Ones to chose to rebuild Zion. This strategy by the Architect worked, until Neo came along.

Q: HOW DOES THE MATRIX HELP THE MACHINES?
A. The humans in the pods must accept the matrix virtual reality program as "real" to have the correct mental state to produce energy and to have mental stimulation to stay sane.
Architect: "nearly 99% of all test subjects accepted the program, as long as they were given a choice."

Q: WHEN 'IMPOSSIBLE' THINGS HAPPEN OR THE MATRIX IS RELOADED, WHY DON'T THE HUMANS REALIZE THE MATRIX IS FAKE?
A: While there may be memory wipes of any person who witnesses something "impossible", most people would try to mentally process the events in a way that would reinforce the Matrix's reality. The system uses the media to portray the rebels as "terrorists"… Also, as the Oracle explains in Reloaded, the system allows blue-pillers to perceive things beyond its control as supernatural…

When there is a "reload", the humans connected to the matrix could be put into a dream state. Also, human memories can be changed the same way Trinity learns to fly a helicopter in "The Matrix".

*************
THE POWER OF NEO AND SMITH AND THE MATRIX NETWORKS/WORLDS

Q: WHAT IS THE SOURCE?
A: It is a machine network central ("mainframe") computer.
Oracle; "... The Source."
Neo; "The machine mainframe?"

Q: RAMA IN THE TRAIN STATION TALKS ABOUT DIFFERENT WORLDS. WHAT ARE THEY?
A.

                                       Sentinels
                                           |
+-------+ +~~~~~~~~~~~~~~+             +-------+ 
|Matrix |~|Train Station |~hidden link~|Machine|
|program| +~~~~~~~~~~~~~~+             | City  |
|network|-----main link----------------|SOURCE |
+-------+                              +-------+
    ~                                      | 
Zion ships                      Architect's room

This shows how programs can move from the machine city networks to the matrix computer program.

Q: HOW DOES NEO GET HIS SUPER POWERS?
A: Neo gets his power by connecting to the Source computer and partially controlling it. Then he is powerful with things that the Source can connect to directly, the matrix and sentinels. But he doesn't have super powers in the Train Station which has a connection hidden from the Source.

Q: WHY IS NEO MORE POWERFUL THAN MORPHEUS?
A: Morpheus and Neo have similar thinking but only Neo has the One code which allows Neo to have greater power in the matrix.

Q: HOW DID NEO STOP THE SENTINELS?
A: Since Neo is the One, he is connected to the Source… Being connected to the Source gave him the power to short their fuses.

Q: HOW DOES NEO MAINTAIN HIS LINK WITH THE SOURCE OUTSIDE OF THE MATRIX?
A: The Machine world must be covered with transmission receivers so that the machines can communicate with each other and the "Source" wirelessly. All Neo has to do is be in range of one of these receivers. The "One" code allows him access to this network.

Q: HOW CAN NEO MAKE A WIRELESS CONNECTION?
A: There may be technology in the large connector in his head which allows wireless communication using the One code.

Some believe that Neo stopping the sentinels means he's in another matrix program. But Neo can connect to the Source or machine central computer which allows him to control the sentinels;
Neo; "Tell me how I separated my mind from my body without jacking in? Tell me how I stopped four sentinels by thinking it."
Oracle; "The power of the One extends beyond this world. It reaches from here all the way back to where it came from."
Neo; "Where?"
Oracle: "The Source. That's what you felt when you touched those sentinels"

Q: HOW DOES NEO END UP IN THE TRAIN STATION?
A: Since he was connected to the Source, he attempted to stop the Sentinels. He succeeded but was not ready for the power. He slipped into a coma, and therefore his command did not reach all the way to the Source and back.

Q: WHAT IS THE TRAIN STATION?
A. The Train Station is the connection between Matrix and one of the computers at the Machine world. This connection is 'illegally' established by the program called "Merovegian".

The Train Station also has to be more than a connection point. I am sure that Rama and Kamala don't have "Residual Self Images" (look like humans) while in the Machine World. … The Train Station must be a program that somehow takes their Machine code and turns it into Matrix code which gives them "Residual Self Images".

Q: WHY DOES THE NEW/STRONGER SMITH EXIST?
A: When Neo was 1st resurrected in the Matrix, Smith became something totally different. He was freed from being an agent... The Architect used him to balance the equation when Neo got stronger.

Some think Smith became powerful only because Neo changed him. Smith says; "Perhaps some part of you imprinted onto me" But the Oracle also talks to Neo about Smith; "He is you. Your opposite, your negative. The result of the equation trying to balance itself out."
The Architect is trying to control the matrix. The Oracle explains the Architect's reaction to human choice; "To him, they are variables in an equation. One at a time each variable must be solved, then countered." The Architect knows that through his design some computer program will become powerful enough to balance Neo's power. By chance Smith becomes that powerful program. This balances Neo's power and pressures Neo to reload the matrix.

Q: WHAT IS SMITH'S GOAL?
A: Smith wants to take over not only the matrix network (world) but also the machine city networks (world).
Oracle; "Very soon, he is going to have the power to destroy this world. But I believe he won't stop there. He can't. He won't stop until there's nothing left at all."

Q: WHAT IS THE "SYSTEM CRASH" MENTIONED BY THE ARCHITECT?
A: The system crash happens if Smith destroys the machine computers.

Q: HOW DOES SMITH GET INTO SOMEONE'S BODY OUTSIDE THE MATRIX?
A: Smith infects Bane right before Bane exits the Matrix.

By Smith infecting Bane's virtual body he infects Bane's mind in the physical world. Then Smith connects to Bane's physical body with a wireless connection. This explains why Neo sees Smith's image inside Bane's body". This is possible due to Neo being connected (wireless) to the machine network and seeing all of Smith's connections, including Bane.

Q: IF BANE IS SMITH, WHEN NEO KILLS BANE, WHY DOES SMITH STILL EXIST?
A: Bane wasn't the original Smith,… It is the same as killing one of the Smith clones.

*************
THE END OF "REVOLUTIONS"

Q: WHY CAN'T "MIS-BEHAVING" PROGRAMS LIKE SMITH BE EASILY DELETED?
A: Programs can hide in the matrix.
Oracle; "usually a program chooses exile when it faces deletion."
Neo; "Why would a program be deleted?"
Oracle; "Maybe it breaks down. Maybe a better program is created to replace it. It happens all the time. And when it does, a program can either choose to hide here or return to the Source."

Q: WHY DOES THE ORACLE LET SMITH TAKE HER OVER?
A: She figures if she allows Smith to be even more powerful than ever before, it will be too difficult for the machines alone to delete him… Smith doesn't only have the power of the Oracle, but of Sati and Seraph too. Therefore, this leaves the machines only one choice; to allow Neo to kill Smith in return for peace.

Q: WHY IS SMITH DESTROYED AFTER NEO IS TAKEN OVER BY SMITH?
A: * Smith and his clones can be seen as an exile program in the matrix that can hide from the Source. But Neo (while inside Smith) connects Smith to the Source (with a connection provided by 'Deus') and this allows the Source program to delete Smith and all of his clones from the matrix.
* In "Reloaded" Smith returned after being 'destroyed' in matrix 1. Why? To balance Neo's power. But in "Revolutions" Neo, while inside Smith, goes to the Source. So, because Neo is no longer in the matrix, there is no need for Smith to return to balance Neo.

Q: WHY DID THE MACHINES AND THE HUMANS NEED TO DEFEAT SMITH?
A: Neo tells Deus; "The program Smith has grown beyond your control. Soon he will spread through this city, as he spread through the matrix. You cannot stop him." Smith would eventually have taken over the machine city networks and the Source. Smith's virus programming would crash the pod life support computers killing the humans connected to the matrix.

Q: IS NEO DEAD OR ALIVE?
A: Is he dead? When Neo is inside Smith, Smith is deleted from the matrix to the Source. This deletion clearly looks like it kills Neo's physical body. There is nothing in the movie that tells us that his body will be healed.

Q: WILL NEO BE SEEN AGAIN?
A: From the final scene;
Sati; "Will we ever see him again?"
Oracle; "I suspect so....Someday."
They are talking about a time when they will see Neo again and not if his physical body is alive. The anomaly of the One will keep happening. The Oracle is guessing that a new One could have the personality of Neo. This is possible since Neo's mind was absorbed into the Source of the machine network. So, in the future his mind could be put into a new body.

Q: WERE ALL THE HUMANS IN THE MATRIX KILLED?
A: Smith did not kill all the humans connected to the matrix when he took over the matrix "world".
* The Architect and the Oracle talk about peace between humans and the machines. This is only possible if the humans survived.
* The Oracle also mentions the 'others'; "The ones that want out."
Who wants out in these films? Humans in the matrix. So, again humans must have survived.

Q; WHY DON'T WE SEE HUMANS AT THE END?
A: Images from humans are being rebuilt because of the 'reload' of the matrix program caused by Neo's 'code' being absorbed by the Source.

Q: WHY DO WE SEE SATI AND SERAPH?
A: They are exile programs hiding in the matrix that cannot be erased by the Source. They are not changed by a reload of the program.

Q: ARE THE HUMANS STILL TRAPPED IN THE MATRIX?
A: The Architect (and the machines) agreed that the humans at the end of "Revolutions" have the choice to leave the matrix. The Architect says about the 'others' (humans who want to leave the matrix, see previous answer); "Obviously they will be freed."

Q: IF GIVEN A CHOICE, WOULDN'T EVERYONE REJECT THE MATRIX PROGRAM?
A: Would humans choose a comfortable life in a virtual reality (VR) world over a harsh life in a real world? A VR world could be as addicting as a drug.

Imo at least, BB ;-)

To me it's a tricky thing to try to extend/soft reboot any major franchise.
From what I've heard there is a dilemma imo.
-  The Warner Bros. studio does not want the Wachowskis involved in another matrix movie (due box office failures).

You make good points. Maybe the studio and a top notch director/writer can make a matrix sequel work without Keanu. 

BB ;-)

Yes, there is a mental blindness with the Architect which does not fit his great intelligence. 
On the other hand, there are examples of brilliant people being in denial about things.
The Oracle has been able to see answers to problems which the Architect could not grasp. 
And because of his denial/mental blind spot, he cannot give her credit. 

Imo at least, BB ;-)

In a way yes, the Architect has an idea that the Oracle is solving problems that he can't figure out. 
Yet, the Architect is being a jerk about it. He grudgingly acknowledges that she's done things and then rambles on about how great he is and how perfect his creations are. 
An egomaniac if you ask me. 

Imo at least, BB ;-)

That was because he was clearly nowhere strong enough to, and also because he did not even know the extent of his own powers.  Moreover, as Neo was kind of 'hacking' the system himself (in order to rise to the level of 'The One'), it was clear that there were still things he could not hack / levels of control he could not attain.  Lastly, and more pertinently, Neo himself was a part of the Martix -- "another system of control" -- the sixth iteration, in fact; and so was not designed to take on the Machines directly.  The meeting at the end of the trilogy was a happenstance encounter that the Machines has not anticipated (see: the unquantifiable problem of choice) as the balancing anomaly to the Smith program that had gone rogue-cum-turned-malware. 

The prophecy was not a direct gospel, verbatim telling of what events would transpire.  Rather, a guide -- something that's touched on in the film/s later on.  I believe the actual line was "...bring an end to the war".

This is perhaps the weakest subtextual element of the film, as it defies any semblance of scientific logic.  As you've stated, the people of Zion had their own energy source and there are myriad ways in which a super-sentient A.I. could gather power (e.g., erecting solar panels in orbit -- a literal, theorised proposition for civilisations on The Kardashev scale).

Fundamentally, where the "Duracell" argument collapses, is when it confronts The Law of the Conservation of Energy: you cannot get more from less.  Draining humans for power while feeding them to one another in order keep the cycle going (to say nothing of the 'chicken or the egg' quandary, of which came first: the 'feed' or the 'livestock'?), all while extracting enough energy for oneself (and those giant farming 'tentaclebots'), is impossible... even in stretched-to-breaking "movie logic" terms.

MacGuffin; and without the humans, there are no films! 

In this sense, comparable 'man versus machine' sci-fi films, like Terminator, are far more grounded in reality than The Matrix was.

The former is a "guide" for 'The One'; there to encourage him to follow the general path set out by The Architect -- the Machine's "coder" -- so that they can eventually learn more about that bug bear of theirs: choice.
 
The Oracle is the program that learns from humans, in order to adapt The Architect's future Matrix revisions to the infinite variables associated with the red herring of human choice.

He's a 'code gatherer' for the Machines, which / who they then parse and use to fashion their new and improved 'Matrices' upon.

The Architect permits him to be found and thus to be rescued.  The only anomaly here was the Smith program, which began to develop its own 'A.I. within the A.I.', if you will, and so threw a spanner in the works, that eventually elevated Neo's worth beyond just another Machine 'tool'.

The Agents aren't a part of the learning protocols of The Matrix program.  Rather, they're the "cops" there to police the "red pills" who are permitted to emancipate themselves (in line with the The One's pathing), so that they do not run amok and 'break' the system from the inside out.  As such, they have no understanding of the role of "The One", and so continue to fulfil their own protocols. (...until Smith begins to learn above and beyond "the purpose" he was originally created for).

It's all the 'beta testing' cycle.  With each iteration, The Matrix is refined, made to run smoother and closer to the vision of The Architect.

That's the purpose -- to reload the undated version of the system with Neo's code (findings) incorporated, in order to make it better than the previous version.

The destruction phase is a part of the cycle of Matrix revising, that takes place each time Neo returns to The Source to disseminate his code into the new Matrix.

Because they did not have an object of infatuation ("love") that Neo did (Trinity), and thus they simply chose to preserve the homo-sapien species -- the logical choice, which The Architect could easily anticipate.

It helps them learn about what makes humans tick, thereby providing them tools by which to improve their digital imprisonment device for humans.

They do... some do.  As was depicted with the "dé ja vu" scene in the first film.  It's just that the changes are subtle and most dismiss the anomalies as whatever figments of their imaginations a given episode or incident aligns with.

The 'brain' or mainframe of the Machine.  The literal CPU running The Matrix.

They're operating through 'back door' program paths that permit their travel in and out of The Matrix (to The Source or sub programs, like the Merovingian's lair) without being observed.  They're an analogy of what N.S.A. do to hack into any and all of our applicable devices today.

He begins "to believe" -- i.e., he starts hacking The Matrix himself.  All the "red pills" hack to system to whatever degree.  However, in the case of The One -- being the 'code gatherer' for the program -- he is permitted to rise above and beyond the other comparative nonentity escapees.  His powers outside of The Matrix are meant to represent a kind of telepathy that he beings to develop, allowing him to 'remotely' interact with the Machines -- perhaps alluding to the flip side of what Smith did when he entered into the noggin of that hapless crew member and took over his corporeal form.

A kind of merging of the two entities.  Or, even a battle between the two, where the Machines use their technology ("jacking in") to, in a sense, become human; while human's take the evolutionary scenic route and develop supraliminal abilities that can give them the ability to "jack in" without wires, brain plugs or Toejam & Earl telephones.  It's a dance of adaptation between the two factions.

Morpheus is just another pawn and not an integral part of the program's purpose. He's likely a human with inordinately developed perspicacity that allowed himself to be freed (or to free himself -- the forthcoming film/s may clarify this).  He is obviously hunted by the Agents, so -- unlike Neo -- was not in 'the loop' with the imprimatur of The Architect.  He was just someone who happened to be there for the sixth iteration of The Matrix, that the films we were presented with, chronicled.  He was more devout than some of the others, and this was represented through his superior, in-Matrix martial arts skills.  Other than that, he was just another "red pill" who like had predecessors that may have shamed him in both devotion and skill.

It was the first sign of him developing telekinetic or ESP-like abilities.  Later versions of The One may be even further developed in this department -- it all depends on the direction the narrative takes.  I saw this as a representation of the evolutionary direction a human being, whose every sense but imagination is stifled.  Kind of like how blind people have good hearing etc. -- no tactile senses = heightened mental abilities.

As above.

As above.

He himself inadvertently enters the 'back door' realm, as a result of the shock to his system after the sudden realisation of his in-Matrix abilities manifesting in corporeal form.

Was already covered; but can be seen as a 'filter' for that which passes through -- in order to ensure nothing that may jeopardise the framework, can enters.

As he begins to learn beyond what he was coded for, and then goes rogue -- finding his "purpose" -- in this process, he starts exhibiting virus-like traits.  Smith is not "stronger" per se, only that there are more of him (many more!) and eventually he consumes so much that he all but becomes The Matrix.  I'd imagine it like letting a PC get so overrun by malware, that every normal function is rendered inoperable--due to how overwhelmingly corrupted its files have been rendered.

Smith had no goal -- as he often alludes to.  He's just going with whatever compulsion his ever-spreading code brings about.  For example, after 'absorbing' The Oracle, it's clear he 'sees' more than he ever understood before, and thus is driven by a different motivation than earlier.  He's a virus.  He consumes until there is nothing left to consume.  His goal perhaps most aligns with nihilism.

Like with any program, if processes take place which have no provision in place for, they can result in system crashes. The system cannot compute what is taking place and thus bugs out and shuts down (CTD).  If Neo does not choose one or the other door in The Architect's room, the system with crash.  If Smith continues to his ultimate end, the system will crash... and so on.  Whatever The Architect has not coded for prior to loading The Matrix (providing the anomaly is serious enough), can cause it to crash.

Seemingly he reprograms (insta-brainwashes, M.I.B. / red flashlight style) the guy through aural means.

Smith had multiplied by then and so was not embodied in any one of this clones. Otherwise, Neo killing the 'master' Smith would have killed the lot.

They're a virus and they spread.  Anyone who's ever had to chase a virus through their PC, can surely relate...!

She calculated the outcome either way and saw that Neo would defeat him in the end were she to give Smith her "eyes".  Also, Smith had found her hideout -- that was here defence; not martial arts or firearms.  She was the empathetic program arm of The Matrix system, not a combative one.  Of course, the film's 'hammer' was chop-socky combat and firearms play, so everything does indeed look like a 'nail' to the viewer.

I think it was tacitly made clear that, by martyring himself to the Machines, Neo would be implanted with an "anti-virus" that would kill / clean the system of the Smith virus -- provided the game played out as it did.  Hence why he still fought Smith to that pointless Dragon Ball Z conclusion -- in order to lure him into taking the bait with minimal arousal of suspicion.

He had become an all-engulfing virus -- self-explanatory.

In corporeal form, seemingly dead.  In The Matrix, anyone can be whatever -- and he was a tool of the system, after all.  So, for all intents and purposes, he could manifest again... but, likely would not.

As above.

No.  The system remained in stasis at the conclusion of the third film.  The exchange between the The Oracle and The Architect implied it was only and armistice of sorts, nay end to their war.  This could mean that their war could erupt again and more could die.  But, as the film stated, all those who wanted to leave the system, could ("red pills", that is) and Zion would be left as is...

Directors' vision.

Perhaps to convey the 'human side' (Sati) of the Machines, thereby reconciling its decision to cede to the subjugated humans' demands for peace.  Or, simply because Zion had been devastated, and the Wachowskis felt that leaving the viewer's with those images, was not the way they wished their opus to conclude.

Those who do not know they're trapped, are "inured" and so aren't technically trapped at all.  While the "red pills" -- those cognisant of their predicament and who want to leave -- are free to leave; as was stated in the final scene of 'Revolutions'. 

Hardly.  People are given a choice to become doctors and astronauts, but few pursue these endeavours.  Why would people want, not only their entire world, but literal reality uprooted, based on something some cryptic goth-punks whisper to them at an Ecstasy addled rave? 
("Blue pills" in.  "Red pills" out.  The End.)