After playing through games like inFamous and Prototype, I do think there is potential for a decent Superman game. How about this:
Open-world style. The game world would consist of Metropolis, plus a lot of country side areas (like the worlds of GTA:SA or Just Cause 2). There would be other areas that the player could fly too, like the Fortress of Solitude (which you would get to by flying to the northern edge of the map) or even SPACE. Quick transport would never be an issue, seeing as how you can just FLY EVERYWHERE.
Most of the game would take place in the city, but the countryside would play host to things like the opening and tutorials, as well as the occasional large scale boss battle. Just imagine a mission where you're trying to slow down Doomsday as he makes his way to Metropolis, then fighting him in the city streets.
The issue of character building is a tough one. The systems seen in inFamous and Prototype, unlocking powers through the story missions, don't work with the Superman mythos. On the other hand, simply giving him a full set of powers at the start would make a for lengthy starting tutorial, and wreck game balance. The best system I could suggest would be something in between. You would have ALL the powers available at the start, BUT they would be weak and unrefined. You would gather XP from story missions and side-tasks, and would spend that on upgrading, say, the range and damage of your Heat Ray.
The story would involve some shit with Lex Luthor. Because why the fuck not? Also, a Luthor-centric story shouldn't stop us from bringing in some other classic villains. WOOHOO Brainiac and General Zod!
On the side, you could also engage in foiling robberies (by just grabbing the robbers getaway car, and dropping it a prison courtyard), saving people from burning buildings, throw down with hoodlums.... You know, Superman-y stuff.
OH, and time trial races where YOU FLY THROUGH RINGS! Gotta have some of those!
