is that they're almost all classless (at least all the ones I've met). The superhero genre is precisely where a classes+feats+multiclassing model should shine. Something like True20 or d20 Modern, both of which had very generic classes and special-abilities-from-a-menu every level, would work perfectly with a somewhat doctored (ie, upgraded) selection of feats. At the end of the day, it mostly boils down to fighting-types (Wolverine, Hulk, Thor, ...) and wizard-types (Doctor Strange, Xavier, Scarlet Witch, ...). The gear-users (Batman, Iron Man) are mostly actually fighters, while the blasters, speedsters, and one-spell wizards like Nightcrawler are more like a 50/50 split with all of their 'magic' focused into one thing. I think it could work.
By comparison, yes, Mutants and Masterminds (which is based off of True20) lets you play as basically a normal human with one super-thing they can do really well. Buuut... point-buy adds a lot of complexity to character generation and balancing it is practically impossible. I don't think it's worth it, especially when most superheroes do fall into an archetype or combination of just a few archetypes.