The difficult thing about a Superman game is presenting a credible challenge to a nigh invulnerable protagonist.
There's only been 2 good Superman games made to date. The Atari Superman and the SNES Death and Return of Superman game.
I think it would work if if you played up the intergalactic elements. Set the early part of the game on Earth where all the enemies are easy and the challenge is presented by protecting others rather than worrying about damage. Sure you'll have a regenerating health bar, but virtually nothing on Earth will be able to make it deplete completely.
Then the second part of the game takes you to another solar system, which doesn't have a yellow sun. Superman's powers are lessened here and the enemies are actually a threat. On this planet Superman discovers a plot involving Darkseid.
Then the game progresses to Apokolips where Darkseid is planning an invasion of Earth. Once again your powers aren't at full strength, but you can still fight Darkseid's minions.
Then the last hour of the game takes place on Earth during the Apokalips invasion. Superman has his full power back from the sun, but Darkseid has unleashed the full force of his army as well as releasing Doomsday from his prison forcing a full powered Superman to fight villains who actually test his limits.