I've been playing Batman: Arkham City all week, and it has really inspired me to do something similar -- except instead of having it revolving around Batman and his rogues gallery -- I'd love to have it set in the Marvel universe instead. I can either play as Wolverine or as Remy "Gambit" LeBeau. The idea is that a prison has been built to keep these mutants away from the world's population. Their mutations are heavily controlled to the point where someone like Storm could only create a light bit of rain or Shadowcat is unable to phase through the prison's walls.
Sentinels patrol the prison, keeping the mutants in check. However, they act more like referees than prison guards -- as long as they don't try to escape, they would gladly watch the mutants fight amongst themselves. Mutant gangs fight for control, and I have no problem playing some of them (I have an idea of having Colossus turned in to an evil gang leader who has an ever-growing turf, for example).
I have a couple of pairings I would like to play out, if anyone is interested.
1* Gambit x Rogue
2* Wolverine x Jean Grey
3* Gambit/Wolverine x OC
If we go down the OC route, then I figured we could either have her being in the latest batch of mutants to be thrown in to the prison (and saved by either Wolverine or Gambit) or have her forced to work as a prostitute that Wolverine or Gambit uses on a regular occasion. Hell -- if you catch me on a good day I might play as them both.