There are d20 System games without classes, Crash. Mutants & Masterminds, for instance, has a point buy system for chargen much like Shadowrun's, though with different values, of course. It is actually one of the easier superhero systems to pick up, especially when compared to things like Hero System, Heroes Unlimited, BESM, and others.
Personally, I find M&M 2nd to be the best of the M&M editions. Flexible enough that you are able to do any character you want, but firm enough that you aren't going to have someone be Goku, but with invulnerability.