I've never played a really good superheroes system, but I recall being particularly frustrated with Mutants & Masterminds. Very detailed rules for powersets, but so many balance issues. Like, I think there was a transformation ability where, for a fairly low investment, you could essentially spend all the rest of your resources twice over, once for each of two forms, with the ability to switch between them very easily.
And in play the different powersets were difficult to synergise and very tough to build balanced encounters around, and in a party with vastly different modes and speeds of movement it became all but impossible to avoid splitting the party.