MCU Reboot: How would you do it?

Since all the MCU movies are pretty close to the source, I wouldn't really do origin movies for characters that already had theirs in the MCU. I'd do sorta origins that add in characters from X-men, FF and Namor. I'd start off with Cap being the 1st movie, in WW2. Do the Invaders as happening during the time he was with the Howling Commandos. I'd cameo a young Magneto. This would lead into the Xavier and Magneto movie that establishes mutants as a thing. This would only be about Xavier and Erik. No young X-men. I'd either put Gabrielle Haller or Amelia Voght as the female lead. These would be the only movies before modern times. Just to establish the world again. The next movie would be Avengers with no Cap. It'd pretty much be the same as the Avengers we got except no Cap, but Ant-man and Wasp would be there.

Then the FF origin movie. Have them as SHIELD agents. R&D (Reed), quinjet pilot (Johnny), radar and comms (Sue), and security (Ben) agents. Sue spots something in space, but no one thinks it's relevant. Setting up how no one pays attention to her (invisible). Probably some more important thing like a news feed about Victor doing something in his country. She goes to Reed, who brings in Ben. With Johnny's help they steal one of the space-worthy quinjets. Cosmic rays, things happen, they get powers. Give them a minor villain to fight just to have a end battle.

Thor, Iron Man, and Hulk (live action version of Hulk vs with Wolverine) movies.

Spider-man would be pretty much the same as barkingbaphomet describes. He's recently become Spider-man. Uncle Ben's murder would be a flashback/nightmare he has. I put the FF movie (and movies in between) before this just to set them up in the world and have Peter want to join them. End credits scene would have the media thinking he was a mutant and that he's a menace and establish that mutants are bad. Pull out to a show a tv and pan around to have our 1st look at the X-men watching the news.

X-men movie would be the comics First Class going up against Magneto and the 1st Brotherhood from the comics. No Mystique and no Wolverine.

Since all the major players would be established, I'd have 2-3 movies a year from each of these categories (main Marvel, Spider-man and X-men). Except Spider-man having a titled movie every 2-3 years. Rotate him with other characters like Dr Strange and Black Panther and the New Warriors, etc. On the years with no Spider-man movie he either appears in someone else movie or is mentioned in the background. The X-men I'd rotate like X-men team (x2), Wolverine, Rogue (Brotherhood movie), X-Factor (government's mutant Avengers), X-Force... I'd do the movies like Spider-man Homecoming and Civil War in that any of the other characters could appear in the other movies. Keep reminding us that the world is connected and to keep tabs on what other characters are doing.

And I'd so advertise the next movie in the current movie (unless it's something like Guardians). Like in the movie with SHIELD ties (Avengers or what have you) before the X-Factor movie, I'd drop in a few lines about how they are developing a mutant team to police mutants because of what happened in the Rogue movie. I'd have Mystique get caught and thrown in the Raft by the Avengers in an opening scene before the Rogue movie.

Shirley Ben should be the pilot?

SHIELD was a big part of the MCU in the beginning.  Especially with monitoring alien threats.  It also would make it easier for them to get something that could take them into space and have an adventure before they got their powers.  Then I wanted them to actually work for them in the field that would closely go with who they would be after they got their powers and formed a team.  The thing I see with Sue is that she's smart and a high level hacker (why I put her on a computer), but her father pulled some strings and put her in a position that would keep her out of the way and safe.  I picture her part at the beginning of the movie like Rachel Taylor in the 1st Transformers.  Nobody is listening to her so she goes to her friend Reed.

A pilot, yes.  But would that matter after?  Unless you keep him going on about how he can't fly anymore, then it wouldn't help after their change.  I mean, you can be a field agent and still know how to pilot a quinjet.  I'd just have Johnny be that hot shot show-off pilot.  The one that tries to get them out of the cosmic waves* by doing amazing maneuvers.

*Yes, more than one so it wouldn't be the same old "must go faster" to get away from it.