When I first heard that they were going to make Superman Returns, I plotted out a trilogy in my head. To this day, I still think it could work as a trilogy very well, so what the hell, I'll just post it here to see what you guys think.
Note: In general, trilogies stick to the rule that the first film is about origins, the second film is about an identity struggle, and the third film is about chaotic war that forces everyone to step up to the plate and "be a man". So keep that in mind here while you're in line for a long, long read haha.
FILM #1: Jor-El on Krypton tells everyone that the planet is doomed, but Brainiac (the "Brain Interactive Construct" artificial intelligence version from the animated series) informs them that he's wrong. Krypton blows up, Kal-El is rocketed to Earth, he grows up with the Kents, starts developing powers, etc. Present day, Kent has just gotten a job at the Daily Planet and meets Lois Lane and Jimmy Olsen. Clark is trying to figure out how he could be best suited as a guardian of peace. Meanwhile, Luthor is involved in government contracts for weaponry and he has two main projects that he's working on: Metallo and Parasite, both of whom are being fueled by "foreign substances" (ie, Kryptonian technology, Kryptonite, so forth), and they're the "secret ingredient" that Luthor doesn't want to let anybody know about. Generic action sequence, where people are introduced to Superman...preferably a scenario where he helps Lois. They dub him Superman and he steals Luthor's thunder. Superman starts putting a major dent in the crime in the area, breezing through thugs like nothing. Luthor decides to test out his projects and *some incident takes place*. Lois decides to investigate, which is how she gets into danger later on. So on and so forth, eventually, this leads to Metallo being the enemy that Superman can "toss around" so to speak, with Parasite making him weak, since, you know, strength-theft is a part of his power. In the end, Superman wins, Luthor is locked up, etc. Twist at the end: Brainiac somehow figures out about all this Kryptonian technology, Kryptonite, and Kal-El.
FILM #2: This film essentially deals with Clark's identity, of course. He feels homesick, he struggles with keeping his secret from Lois whom he loves, and on top of that, Brainiac shows up and tries to set up this whole "I can help you learn about Krypton" type of thing. Quite possibly, if you have the time, Clark is tested by Brainiac when he's sent to War World and has to fight off Mongul's people. This would only be one fight scene, though, and it might not be able to work time-wise. Brainiac's main motivation is, as always, to obtain all the information on the planet, upgrade his own program with other technology, and then annihilate the evidence. Luthor tries to work out a deal with Brainiac. Both Luthor and Brainiac are just keeping the temporary deal because they think they can screw the other villain over when they've outlived their usefulness. By the end of the film, the public thinks Superman is just too powerful for his own good, as in the final battle, something terrible happens because of his strength. He feels guilty about it. Luthor is let loose from prison (or pardoned, somehow) and Brainiac is killed...but, anybody that knows this incarnation of Brainiac knows that he lives on in another program somewhere. Clark abandons hope for a relationship between himself and Lois.
FILM #3: Quite simple, Brainiac brings reinforcements...namely, Doomsday. Luthor has to work with Superman to try to take care of the beast. In some way, Luthor helps outsmart Brainiac (not by much, obviously, as that would be overkill for such an intelligent computer) through some sort of "human-only" thought process. This keeps up the parallel between himself and Superman, as Kal-El isn't human. Clark defeats Doomsday but dies in the process. Somehow.....maybe through something Brainiac leaves...maybe through something in the Fortress of Solitude...maybe through Luthor himself, who knows yet as I haven't written the damn thing haha....Clark ends up regenerating and is alive again. He and Lois get together, and all is well in the world with a Superman who now knows without a doubt that the world needs his watchful eyes.
Now, I originally thought of that in about a 4 minute time-span, and this was a while ago, so I forgot a lot of the little details. But yeah, I think its self-explanatory how well it works haha. The only regret is that there's no Darkseid or Bizarro, but hey, I think having five (or six if you can fit Mongul in there) major villains is pretty damn good for keeping up the story and not overloading it for the sake of having more fight scenes. Story is what makes a good film, not "more explosions".