Superman's abilities are so big, you have to design gameplay around it... you can't shoehorn him into a predetermined formula, because he's just plain old too big.
The first thing is that a lot of superman's 'feats' don't occur inside metropolis, so confining him to that city means you have to either send tons and tons of randomness into his city, OR use Metropolis as a 'hub level' and spread the action out to different locations. Locations that lend themselves more towards level design.
Which is the second challenge, how do you design a level for a flier? The basic answer: don't make an action game. Make a challenge game, perhaps a large puzzle filled with deadly obstacles that you can punch to death. Since you can't restrict his movement with obstructions, restrict him with time and processes to complete objectives.
The SR game did get the health right, and the flying right, we have to give them that, though even the flight could use some improvements, it was smooth, fluid and pretty danged fun.
The final challenge for SR is minions/shock troops/thugs. As a rule, Superman doesn't have to worry about these. Usually, Superman goes up against a small group of powered individuals that have a chance of defeating him due to weapons and tactics.
Generally, I'd go with more a multiplayer Map feel for Superman gameplay. He gets to a place, he has objectives, he also has several individuals in the area trying to take him down. He's got to overcome the area challenges, not get whooped and then beat the boss. That's the general idea, add modules and season to taste.
Finally, to me, no Superhero game is complete without making full use of the person's abilities and comic book situation. An infested Metroplis is okay if you don't have time to do the Quintessential Superman game, but if they can incorporate using your sensory powers and secret identity around Metropolis to collect/harvest information/etc, then they'll have something quintessential, and it will be meaningful when your little safe zone gets overrun by something you can't just sit in front of and eat bullets from.
Can you imagine how much fun that would be? After a particularly challenging run on Apokalips to fly in front of some bank robbers and just let the bullets bounce until they run out. Good times.