The Dark Knight Rises;
Bruce would've been active as Batman at the start of the film. The 8 year gap comes after Bane breaks his back.
When people say stuff like this it's like: I'm sure that was the original idea because it's so elegant and makes so much more sense. They
must have changed it for some outside-of-story reason.
Star Wars Prequels:
Without going into the entire story starting Anakin off as a young teenager, so it makes sense for him to be too old, so younglings don't have to be four to justify the line. Also, he'd kind of have a bad attitude, and so when the Council/Yoda says no, it's not a cute adorable little kid, y'know. I'd basically make the whole thing the Clone Wars. Darth Maul would recur, and with General Grievous and Dooku, each be the sort of sub-boss for a movie. I think the clone dopplegangers/assassins is a brilliant idea. Anakin's turn would be based on his justified anger at the injustice in the galaxy and the Jedi's inaction about it, not just Padme dying or some stuff. Also, Padme would have been even more active and hardcore and their romance more... dangerous and less kiddy. They'd kind of fall into each other instead of it being a puppy love thing.
Episode 1 would establish all the players, and start the Great Clone War, Episode 2 would be an all out war movie, Episode 3, set several years later, would be the Last Clone War. The most important thing is that Obi-Wan would be the central character, as we see him grow from a Padawan to a Jedi Knight and Jedi Master. We see him commit to the Jedi ways and not get with Padme which makes Anakin's failing her all the more spiteful to him. We see him strive to be a great teacher for Anakin and simply fail because of his own hubris, his own overestimation of his bond with Anakin, not unlike what we saw in the films, but a bit more pronounced.
Man of Steel:
I'd have limited the number and resources of the Kryptonians and had Kal-El meet them as friends, learn about his history primarily from them and then feel betrayed and have to fight them when they decide the Earth is theirs for the taking. His costume, at least for this first installation, would be created by Martha, and be pretty much just as it is in the comics, and the fact that it is "hokey" would be a plot point, and part of the charm of the character. He'd battle a gauntlet of aliens. I also wouldn't have him fly until the very end, Zod would be the one who taught him to fly, and the Kryptonian scientist. In fact, I think the whole thing I'd take a little more from Kal-El's perspective, so not so much Jor-El focus during the film. Zod would play the whole 'I knew your father come takes his place amongst us' thing. There's a lot of things I liked about this film, but some of the sci-fi babble seemed entirely unnecessary.
The Matrix:
The first one was pretty much perfect. The last two I would not abandon Neo's pledge to free all the humans, simply have him pay the high cost in lives. I would add new ideas as things went on, Agent Smith joining the good guys at one point, a machine-sympathetic human faction/crew, the previous one in the cycle appearing, those types of things. Neo would continue to be god-like, but limited by the system hunting for him and quickly tracking down his ship until he figured out how to survive without his body... y'know, him being the One. Cue Neo's majestic return, and the ultimate destruction of the machine empire with a grand finish of millions of people walking out into a newly greening post-apocalyptic world without computers.
Captain America: The First Avenger
Speaking of Hugo Weaving, I would have made Red Skull a much better/deeper/more menacing character, and a Nazi as much as a HYDRA member. He'd have known Kung Fu, he'd have caught the shield like he did in that 1990's cap movie, he'd have tried to recruit Cap and generally had a great plan. In fact, that whole thing would have been a War movie, much more like other WWII movies than a movie that would have come out during WWII. Red Skull would still have the cube and be using it to power a super weapon of Arnim Zola's design, but HYDRA would be dangerous because they are hard to find, not because of their army. I'd even have the tour take them to Wakanda for a bit. There'd be a couple good action scenes that really show us why Captain America was the greatest soldier in history, not just a montage of his and his buddies. Grendades, guns, shield bounces. Lower-key. The spectacle would go towards set pieces, showing how utterly deadly the weapon can be, a whole mountain coming down around them Hobbit-style, a nuke-styled effect wiping a town off the map, that kinda stuff. Cap would still have the same story, same throgh line except when it got time for Avengers, no one would question his ability to command anything, least of all our attention.
Green Lantern:
Everything. John Stewart with Katma Tui training him taking on Kanjar Ro, The Manhunters and Hallalax. John as a down and out guy who spends the entire movie off-world in a sweeping space adventure, except the first and last ten minutes which take place in Coast City on Earth. Set up for a sequel with Hal and John as buddies taking on the Sinestro Corps, and a threequel that does a toned down War of Light.
Fantastic Four:
Even back then, I would have gone full Ultimate, with a black guy as Thing to boot. Except Ultimate Doctor Doom... 616 Doom or bust, but everything else, young, modern sci-fi, it'd be like Star Trek meets The Incredibles, basically.
The Star Wars Prequels: 
