A Superman game could be very well done. It would especially work if you took some heavy liberties with the character, although it would certainly piss off the fanbase but it would sure make it interesting.
The game starts on Krypton and you're Jor-El or something. You need to get baby Kal to the ship before the planet explodes and there is a war raging all around you. Don't tell me the beginning of MoS didn't look like some crazy videogame already...
Finish the mission, baby goes off into space, huge cinematic explosion. Next scene starts, you're preteen Clark, your powers are kind of developing (doesn't arrive on Earth as a super-powered baby, but rather his powers come to him through adolescence, in stages). Maybe as a kid he can punch pretty good and jump kinda high, but he can still get knocked out/bleed/etc.Hell, maybe he's like Kick-Ass with a slight advantage other than not feeling pain. Most missions are at night since he's sneaking around (against canon, but maybe his parents don't know, etc)
As he gets older into the Superboy years, getting more powerful - still more sneaking around and trying to stay out of the public eye. Maybe he is being chased by the cops/military/Alien Control Squad or something and they have the means to subdue him. He gets caught and has to escape some huge underground compound filled with all kinds of other captured "freaks" (aliens? mutants?) some of whom are rampaging and trying to destroy him/everything else.
Having the game progress from being able to survive dropping a couple of stories, to leaping across a rooftop, then bounding big distances, then ulimately being able to fly into outerspace at superspeed - punching huge holes in things - all of this stuff would be amazing. It would have to be a pretty major undertaking to design and art. In the end it would probably be pretty far off from what people commonly think of as Superman, but it would really be a serious reboot for the modern day that people would be able to digest and would also make for a very satisfying gameplay experience.
DC is probably not too keen on such things however. "Why bother?"