I wish I had something to contribute, but not having actually played Supers! I simply don't have a perspective on this. I see your concern, though, and will keep it in mind as I playtest - hopefully in the next couple of weeks.
I have another "concern" about damage, although it might be more of an observation. When doing my benchmarks for the Marvel characters, I realized that a character like Captain America has more "hit points" (if you will) than a character like the Hulk. Hulk would have a really high Fortitude Resistance, but his other resistances are low, so he ends up with something like 12D worth of resistances to deplete. Captain America, on the other hand, would have something like 16D. I'm wondering if your observation kind of evens things out a bit. Sure, Hulk has fewer resistance die to deplete, but the high rolls he gets on Fortitude and Armor might make him tough enough for the genre.
Again - food for thought.