WHY DIDN'T NEO USE EMP TO DEFEAT THE MACHINES?
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 -- t
hat 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.)