I don't have a real feel for doing supers in d20, and wouldn't seriously consider running such a game using the system. It seems to me to be the one major genre that any system designed for normal or heroic level characters will have trouble scaling to, at least if you want to do relatively high-end supers (Superman, Thor, etc.) My primary problem is with the level system - powerful supers don't have to level up to get that way - they just are powerful.
My preference would be to use a dedicated supers system, either SAS-Tristat, Hero or MEGS/Blood of Heroes. Mutants and Masterminds looks very good and could possibly change my mind, especially if it discards levels, but I said the same thing about Traveller d20 and it managed to please me very much while retaining them.