Hey J B!
Some interesting ideas, however my biggest reservation is that you are underselling Doomsday massively. First you have Superman beat Doomsday (or drive him off) then you have Doomsday killed by some Deus Ex Machina meteor impact. The raison d'etre for Doomsday is to kill Superman, but you are just treating him like any old punk villain.
If you just want a run of the mill villain for Superman to beat I suggest you use Bizarro instead, in fact Metallo might work best here. Superman Returns seemed to set up the possibility of Bizarro (the blood on the kryptonite shard) and possibly Brainiac (New Krypton crystals).
My second reservation is that Brainiac doesn't seem to be doing too much, now I know fisticuffs ain't exactly Brainiacs thing, but a big scrap versus a horde of Brainiac drones would be cool. Superman could confront Brainiac and after a hard battle defeat the robot, only to have multiple copies arrive...
However, those points aside, I actually liked the rest of your story.
What I might do is replace your Doomsday with perhaps Metallo, have Metallo defeat Superman in their first encounter (ACT 2), then later have Metallo (now 60 ft. tall) fight against the US Military, before a final encounter between Metallo (now 600 ft.) and Superman in ACT 3.
However, Metallo is of course just a distraction cooked up by Brainiac after the defeat of Brainiac's drones by Superman at the end of ACT 1. But I really like the idea of Lex and Superman on the same team (even if Lex would always try and double cross Supes). So I could see the benefit of pitting Lex against Brainiac. Although when Brainiac gets 'defeated' at the end he is able to "download" into Lex, creating Lexiac (for the third movie).
If think this hits the required action 'beats', although I think what we are missing is a strong opening.
ACT 1 (Opening): ?
ACT 1 (Climax): Superman vs. Brainiac Drone and then multiple Brainiac Drones
ACT 2 (Mid): Superman vs. Metallo (6 ft. tall)...Metallo beats Superman
ACT 2 (Climax): Metallo (60 ft. tall) vs. US Military...Metallo crushes military
ACT 3 (Climax): Superman vs. Metallo (600 ft. tall)...Superman defeats Metallo
The third movie (
The Death of Superman) would feature Lexiac and Doomsday. Lexiac uses satellites to find Doomsday's prison vessel in space, lock on and summon it to Earth where it crashes, releasing the beast. Lex would continue his mental duel with Brainiac (much like the Supes vs. Clark fight in Superman III) for control over his body. Superman would of course die at the end of the movie.
The last scene could be Superman waking up in some fiery 'hell' asking himself "Where am I?" only to have a deep booming voice (off camera) exclaim "Welcome to Apokalips!" Thus we have Darkseid for
Superman Resurrection.