Comics and supers have such wonky rules anyway that I figure the best bet is to find a rules set that works for you and your groups' preferences and treat those rules as the "physics" of the setting. If a rules set says that a character who can run 10,000kph is only marginally "faster" than a high end kung fu master as far as combat is concerned, then so be it: in that universe, kung fu masters are just that awesome, or speedsters just aren't, whichever tickles your fancy. There are so many supers games on the market or OoP but easy to find that no one who likes the genre should ever wont for games (for players, well that's another story).
I am currently starting to put together a M&M 2E PbP campaign that is intended to be used as a backdrop universe to occassional game-day, mini-con and one shot table play and, using the Mastermind's Manual, I figured that combining "Players roll all the dice" and the "Cards instead of dice" rules would give me a solid, comic booky feel. Sometimes, Spiderman flubs it -- i.e. the player rolls low. But in the interest oif the "story", the card mechanic means that instead the player is burning a low card to clear his hand. That means it is intentional, thought out. I think that mnakes for a better emulation of the genre than random die rolls every swing.
The real hard part, IMO, is nailing down the supers sub-genre and general tone. Batman differs from Spiderman differs from Superman differs from Deadpool -- and they are all "super hero comics". Just telling your players you want to run "supers" is dangerous, as each of them could well have a very different definition in mind, from The Authority to Superfriends.
