Here's an idea. I'll leave plot and story for TPTB.
I've thought about ways in which Superman could get a good viable game. They could introduce time limits for certain missions? As well as that you could make use of the Clark Kent persona and switching back and forth? They could introduce the switching as a means for Clark to get into places Superman could not go. Like say Clark Kent the reporter has to go undercover to get intel regarding *insert bad guy here* or something. He could switch in the same way you could switch between Catwoman and Batman in Arkham City, oh and each persona has intersecting and individual missions.
As for health/life for the Clark persona he could take a certain number of blows or perform a certain amount of actions before others realise he's Superman/not normal thus compromising the identity. For example Clark takes a bullet or two and the other guy realises he's not normal/he's Superman=Game over and Start over. Oh as for how the game varies with difficulty, as levels get harder you have less and less places to change between Clark Kent and Superman.
You could also do missions where the player has to possibly choose and triage big natural disasters and super-villain attacks etc and explore the consequences arise when you choose one thing over another. Think the light/dark side or other choice-driven decisions you would make in games like Star Wars: KOTOR or SWTOR.
Basically what I'm trying to say is we need a game which really takes us into a day in the life of Clark Kent/Superman just like how the Arkham games make us get into Batman's mindset. Superman makes life and death decisions and deals with consequences every day, we incorporate that. Clark Kent has to struggle to keep up a disguise and act, let's incorporate that.
If there's a will, there's a way.