We're currently running a d20 game with M&M stuff added on top. It really adds a nice spice to the normally mundane gameplay. Sometimes players go crazy with powers and the DM starts to murder all the players to balance it out, but it's nice. Try it out. I'd say start by not limiting power levels. Maybe a +1 level adjustment for 3 points per level, +3 for 5 per level. That way it still evens out a little.