Wow, I kind of figured that Gemm and I were the only ones paying attention to this thread, and then I turn my back and BAM! Though I have to admit, if anyone else were interested I figured it would be you two.
42 mentioned my main dilemma earlier, and I think it's at the heart of your current discussion: d20, and d20 Modern especially, is based very heavily on early character development during levels 1-4. When doing a superhero game, do you want to let people start off really tough and then focus on character (Palladium style), or start off really weak and focus on a power/character mix (D&D style). I don't think that a focus on power development interferes with character development, but I don't think any of you do either.
The question is how to develop a system that allows you to do both styles of power progression. I was thinking of doing pure feats, with some prestige classes to represent stuff like government affiliation (a la Captain America) and whatnot, but that only works with the "start weak and build up" model. I really think that 42's idea of templates could support the other end, but I'm not sure exactly how.
What I really like about d20 Modern is that it's so open--once we make a few tweaks you'll be able to reproduce just about any comicbook hero, which for me is the acid test of a truly great superhero game (which Palladium fails, btw). Stuff like "mutant" shouldn't be a class because it implies that all mutants are identical except for their powers, and a quick comparison of Wolverine and Spider-Man will prove that wrong.
Wow, my thoughts are incredibly scattered. Anyway, here's a proposal that I invite you to shred:
1. All super abilities are feats, and some have higher levels with bigger prerequisites (flight, improved flight, etc.).
2. There should be a super power "heritage" feat, like the magic heritage feats in Urban Arcana, which do very little in themselves but allow you to eventually gain related powers. Unlike those feats, however, you should be able to pick up a super power heritage at any level (since you could be bitten by a radioactive spider at any time, not just at character creation).
3. Your in-game justification for a power can be anything you want it to be, just like in BESM and HERO: i.e., if you have a ranged power that stuns people you can decide that it's a ray of energy or a big shield that you throw like a frisbee. I'm not entirely certain I like this, but it's the best solution I see at the moment.
4. We will create certain prestige classes that allow access to extra super power feats. This way you can have a Smart Hero who picks up a few super powers (like Spider-Man), or a Mega Hero who focuses solely on super powers (like Superman), or a Fast/Smart/Techie combo with no powers who makes his own gadgets (like Batman).
And templates will...I don't know what to do with those.