They made this game. We all hated it:
https://www.youtube.com/watch?v=1dJXgJ1c4vY
You say that, but for the longest time I'd argue that one of the best super hero games was Hulk: Ultimate Destruction.
https://www.youtube.com/watch?v=uBrdxwFBC64
It really gave you the gravity to feel like The Hulk; when you died in that game it wasn't a single tank firing missiles at you: It was a screen full (well, as good as they could do then) of enemies throwing tons and tons of damage at you.
If they want to have a similar game with Superman then make it simple: The Sun's been blotted out by whatever villain your against. You start the game out really strong and, as the game goes on, you have to master more mechanics because you get weaker. You can even throw in something along the lines of "Kill enemies X or Y, who are solar based, to replenish your powers" or whatever.
As wjowski pointed out...the problem with building a Superman game now is there's already games that let you be Superman AND drive a spacecraft shaped like a Bald Eagle AKA Saints Row 4 AKA The most fun you can have sober.