What about limiting the level of super powers based on the level of game Normal,Heroic,Epic,Super Human. These levels limit the amount of points you can spend on your character but you could also limit the types of powers that can be obtained too. A normal level game has the 'only just super' powers like... oh i dont know.. a few points of natural armour, 1d6 increased strength that kind of stuff, and the Super Human level includes all of the godlike stuff, time travel, indestructible, instant healing.
Anybody seen the movie Mystery Men? For a bunch of 'only just super' heroes this movie is great and full of possibilities...
The main problem that I see with superpowers is that to make the game really interesting there needs to be loads of different powers with lots of different levels of those powers.