My first thought is that about balance. You dont' compare the systems across. The "Superhero" expansion would be something different than the the strong hero or whatever, and yes, a 1st level superhero should be able to beat the snot out of a 1st level fast or tough hero without too much a problem. Just like a D&D character can usually take out his closest equivelent in d20 Modern. OR a d20 modern could take on a CoC character
I'm still working out my feelings between templates and feats. ("I love you both!"). It just seems not right to try and build a lot of superheroes using either method. To me, the D&D system is too much the process. It's hard to get people to make the jump from a feat representing something you do and becoming something you have. Prestige classes do the same thing for me.
for character building, I still keep thinking that point systems will work MUCH better for superheroes than d20 can hope to. Though I like the random attributes. So maybe come up with a new mechanic that works much like feats, but is named and has some important differences. Call it "powers" until I have a better name.
You start out with a defined set of broad powers (which form a tree, sorta like Diablo2), and only in game events allow you to add one (like another energy blast, or a new mutation, radiation, or whatever - each super power causing event adds a certain number of Powers, and no more. Now, not all of those powers have to have any amount of development right away, and as you gain levels you can choose which to develop.
Example, Superman. He has a base of 5 powers: strength, speed, flight, x-ray vision, and heat vision. Some, like speed and strength, are developed more than others. Then, he saves the world (yet again) and the geomancy in play (or whatever, they never explained that satisfactorily) and he gained a whole new set of powers dealing with energy manipulation and magnetism.
Course, then he lost 'em all. Which also plays in. Supes originally has two weaknesses: Kryptonite and Magic. When he gains a new set, he also gained a new weakness: instability. Fixing the instability removed his power base.
So maybe that's more work than most of you want to do, but I think it's the best solution for the feel. It helps with artifact enhancements (Green Lantern: really cool powers, loses 'em all when he loses his artifact, removing his power tree).
Am I being clear enough?