I've been thinking aloud about this whole scaling issue -- specifically, how to handle disparate power levels without climbing higher and higher on the ladder -- and I think I have an answer. Haven't really been able to bounce it off anyone but one loyal reader (at least, I assume you're loyal -- I'm giving you the benefit of the doubt on that one), so here it is for everyone else to take a whack at.
First thing we do is remove the Will mechanic. It's not that I don't like it, because I like it a lot, actually, but it doesn't really work with this new scaling thing. So out it goes, at least in its current incarnation.
Next, instead of three tiers of power, we have five -- 1 to 5, or 0 to 4. Either way. Names are important for flavor, but right now that's up in the air, so let's at least agree on Mundane for the lowest of them and, say, Cosmic for the top end. You get the idea. Like before, skills fit into these tiers and your skill pyramid simultaneously, with some skills designated as Mundane, some as Superhuman, and so on.
When you act against someone else, look at the tiers of your skills. Whoever has the higher tier notes the difference in steps (e.g., Tier 1 vs. Tier 3 means two steps) and replaces that many Fudge dice with d6s. Then roll as normal.
(Yes, this still involves swapping out Fudge dice, but I like that, and I've seen my players like it, so it's a perfectly fine design element as far as I can tell. If you don't like that sort of thing, this won't really work for you at all.)
The point remains to emphasize the difference in power levels between two parties, but still allow them to interact. The latter bit is where the earlier system kinda fell down. More tiers means it isn't easy to just buy up your Mundane skills to Cosmic without spending a boatload of points. How many points, I don't know yet, but it wouldn't be cheap, that's for sure.
So, with that mechanic in mind, look what else we can do. When someone tags your weakness aspect, it reduces your defense by one tier. If your weakness is defined as a "big" weakness (we need another adjective there, obviously), it reduces it by two tiers. Or more, maybe. Maybe it's two and four instead of one and two. The point is, it allows a regular human with kryptonite-on-a-stick to pose a danger to Superman in a way that's internally consistent and fairly elegant. It may even be that the weakness isn't an aspect, or at least not one in the usual sense, but I'm not going there right now.
Why would you have a "big" weakness instead of just a regular one? Because if you take that in conjunction with a super-skill, that super-skill starts with three trappings instead of two.
That reminds me, since I'm rambling anyway. There are three kinds of "negative" aspects: weaknesses, complications, and restrictions. A weakness is what it was in the last post, but complications are limited to things in your personal life -- DNPCs, enemies, secret IDs, and so on. Restrictions are constraints on your super-skills, like "Can't Affect the Color Yellow" or "Power Armor."
Complications and restrictions should have "big" versions, too, with the same extra-trapping trade-off. A big complication means that negotiations for compels start at two Fate Points instead of one. A big restriction is... I dunno. Still thinking about that.
The most shocking thing is probably that I'm thinking of including Diaspora-style stress tracks. Superheroes tend to batter each other a lot pretty casually; it'd feel weird to give, say, the Midnighter a consequence every time he's hit in combat (not that he can be hit in combat, but you get the idea). I like Diaspora's middle ground between SotC and hit point-style stress. It might mitigate some of the potential Authority-scale ultra-violence, too.