I know this has been talked about to death, but this is MY idea for how it could, and should, go. First of all Rocksteady should make it. The reason they decided to go for a Batman game in the first place was because they didn't feel like they could tackle Superman. In the Batman Arkham series they have a level of progression, gaining more gadgets as you go along. I think the best way to do this for Superman is have a game where he's starting out as Superman, but doesn't have all of his powers. Let me explain.
Golden Age Superman's powers came from his alien biology and everyone had those powers on Krypton, they had harder skin and were super strong and fast. Now when the Silver Age began to start he was developing some of the powers he would have later on like flight and began getting stronger and more durable. This must be because he SLOWLY absorbed yellow sunlight compared to the modern Supes. I think the '78 movie explained his powers like that. One part biology, one part yellow sun. Start with Jor-El explaining this before Kal is sent to earth so as not to have just casual fans of Superman who would expect him to have all of his powers from the get go become annoyed with this. As the game progresses, the story spanning several years or so, it shows Superman's reputation grow and his rogues gallery grow as well.
Each new chapter of the game starts with the origin of a villain with said villain being the main villain of the chapter. After you beat a certain number of chapters, let's say 2-3, you unlock a new power. In terms of powers besides strength and would start small like having enhanced hearing to pick up on local crime(Like Batman could in Arkham City) and x-ray vision(Works like Detective Mode, but less highly detailed like Batman's and more like Robin's DM where it just shows hidden stuff and who's armed), then move on to heat vision, super breath, and freeze breath. As far as things like strength and durability go these would be able to be upgraded anytime, provided you have enough XP. Speed would be used more like a straight forward blitz attack, like if you run into an enemy you punch them, but can be used to get around. Leaping would be the main mode of travel for up to the middle of the game where you unlock flying, with the leaping being like Hulk Ultimate Destruction.
Now the main thing is that while you get more powerful, so do the villains. The usual random thugs would be members of Intergang, getting greater more advanced tech to combat Superman and villains like Toyman upgrading his toys to be bigger and stronger or Luthor getting Kryptonite powered robots.
Speaking of Lex he'd be like he is in Superman TAS, a big business man that Supes can't really take down because he always covers his tracks.
Also a unique feature is that YOU get to choose what Superman costume you wear through the game. At the beginning you get to choose between the Kingdom Come costume, the classic costume, the God Fall costume, Superboy's t-shirt look, or the New 52 costume.