I'll make one of two recommendations based on your preferences: if you are completely sold on the D20 Mechanics, I'd recommend taking a look at M&M. If you're looking to try something a little different, HERO would be my suggestion.
Both games are point-based, and both are "effects based", meaning you buy powers in a generic fashion and apply the effects to them as you wish.
In terms of the pros and cons, I think that M&M has a better streamlined character design and power system. It's obvious that the authors have looked at the best superhero games out there, and simplified and streamlined things tremendously.
In terms of combat and playing the game, I have to give the edge to HERO. I've played a lot of M&M, and the more I play it, the less that I like the combat/damage engine. I know that might be heresy in some parts, but that's my opinion. You can look at it for yourself, as the basics of the rules are
here. Many people like the system, but I've found that it doesn't make for a satisfying combat. Any attack that can injure someone at all, has an all too high probability of effectively taking them out of the fight in one blow.
In both cases, these are just my opinions. If you take a look at either system and pick the one that fits with your idea of how comic physics works, you can't go wrong!
--Steve