Now this is a project that I haven't spent a massive amount of time on, with only a couple of miniatures started and a few different ideas and themes buzzing around my head. The setting for my superheroes games will be a universe in which the archetypal "Batman/Bruce Wayne" character is basically a bad guy - actually, the main villain and practically the boss of all the other villains. Now, this is a theme that will be very familiar to comic book readers - just see stuff like Irredeemable (albeit a Superman-analogue rather than Batman, but a similar idea) and Nemesis (which features a Batman-esque villain committing various atrocities). On top of those examples, there's stuff like JLA: Earth 2, where there is a world which is the opposite to the standard DC universe, featuring a Crime League of America featuring all the big names or Wanted (the comic book series, not the terrible film based on it).
In my setting, the "Batman" controls the villains of the world, with the heroes being hunted and attacked at every opportunity. The heroes are fighting a guerrilla war and have been forced to do things that they would have never thought possible - fighting alongside the more vicious villains that refused to bend to the will of the not-Batman, cells being led by what were antiheroes and social pariahs amongst the heroes in the old world (Punisher-types). Expect to see homages to characters that I already enjoy as well as brand new heroes and villains!
If you have any ideas or anything you'd like to add on this subject, feel free to chime in!