I'm pretty certain that if i wanted to run a superheros game, I'd probably start with DFRPG. It would definitely require some tinkering, but I think most of that would be in dialing the number up higher, and re-flavoring some of the mechanics.
For instance, 8 refresh for a low powered, e.g. Daredevil, supers game, going up to 20 or more for Justice League/Avengers level play. Global Supers level play, 20 refresh, 60 skill points, skill cap Epic (+7).
Lore covers super-science, such as gamma radiation, alien tech, fusing adamantium to someone's bones, Time travel, etc. Other minor tweaks to the skill list would probably be in order.
The refresh and compel system gives us a good way to answer the question "How can Batman and Lex Luthor be in the same league as Superman?" Because superman spent about 18 of his 20 refresh on powers, while Bats and Lex have nothing but "normal human" stunts, and probably a pile fate points left over, including the +3 (at least) "normal human" bonus.
It also does great job of giving "With great power comes great responsibility" a mechanical punch.