Making skills from scratch using individual trappings as building-blocks was central to Strange FATE from the beginning, and, by extension, The Kerberos Club (FATE Edition). The process by which those trappings would be put together, though, went through some pretty significant changes.
From the top, I took my cues from Spirit of the Century and Dresden Files. Specifically, I liked the niche protection inherent in the separation of certain skills. Fists and Might, for example. The fact that they're not the same skill (as they essentially are in many other games) implicitly asks the question "Do you want to be Fighty Guy or Strong Guy?"
Sure, Fighty Guy and Strong Guy are probably going to have a lot in common just out of sheer logic. But this isn't about logic -- or rather, it isn't about "physical" logic. It's about narrative logic. In terms of narrative, it's more interesting to have one guy who's great at fighting and another guy who's great at being strong.
Initially, this mean that in Strange FATE, some trappings just couldn't go together in the same skill. You couldn't have one skill that measured both your physical strength (Physical Force) and your facility with punching guys in the face (Strike). Physical Force and Strike were Prohibited trappings! Oil and water! The very idea of pairing them made kittens cry.
As early as the first character-building playtest I oversaw, when Morgan Ellis tried to make a perfectly viable and cool character (one, incidentally, who both of us used in our GenCon scenarios), it became clear that this Prohibited trappings nonsense was just that: nonsense. It was getting in the way of a plausible character instead of facilitating it. Morgan literally shook his fist in frustration, Monarch-style.
So I weakened the Prohibited thing so that instead of it being impossible to pair them, it just made doing so prohibitively expensive. But I didn't much like that, either.
Soon enough, I dropped that bit altogether. Instead, nearly every trapping had a list, some quite long, of Restricted trappings that doubled the trapping's cost if they shared the same skill. This persisted throughout the end of playtesting. I wasn't happy with it for a number of reasons -- the math, the multiple charts, the small print, the page-flipping -- but I couldn't think of a better way to mix trappings while maintaining a sense that some were more compatible than others.
A month or two afterward, I'm embarrassed to say, I was watching the Science Channel one night. Whatever the show was about (not robots or punkin-chunkin', apparently), part of it involved a big diagram of a molecule. You know the kind: black and white and red circles connected by lines in a sort-of linear pattern. For whatever reason, something clicked, and I said aloud "That's how trappings and skills should work." A diagram of trappings connected by lines, with trappings grouped in terms of how much they have in common! The greater the distance between two trappings, the more expensive it is!
Then I realized I'd seen this before in the form of the Quade Diagram from Robin Laws' excellent Mutant City Blues. But this wasn't discouraging -- on the contrary. It was proof that the thing I wanted to do would work. MCB does something a bit different (and very, very cool) with its diagram of super powers, but the basic idea was close enough that I knew I was on the right track.
It's pretty simple, really. Start with a trapping you want the skill to have. If it has a thin solid border, it costs one point; if it has a thick dashed border, it costs two points. Then follow the pathways from that trapping to another one you want for the same skill. Thin solid pathways cost one point, thick dashed pathways cost two, and thick solid pathways are free. You can skip trappings (and not pay for them) but not pathways.
Here's an example:
Leap and Move are pretty closely related -- if you can do one, odds are good you can do the other. It's no guarantee, though; if you want to be the Incredible Frogman, your ability to jump will probably be unrelated to your ability to walk. Move and Dodge are another story, though. If you can walk or run, you can walk or run out of the way; the thick-lined connection between is an indicator of that. However, Dodge is a valuable combat-related trapping, because it lets you use the skill to defend against all kinds of physical combat, assuming you aren't tied down or something. Thus, it costs two points to buy for a skill.
(Yes, the cost is the same to buy both Leap and Move as it is to buy both Move and Dodge, but Dodge has the two-point border because you might not come to Dodge from Move, nor go from Dodge to Move. One's ability to avoid any attack of which one is aware can be flavored a million different ways in a supers game.)
The diagram solved every problem I had with the way I'd been doing skills. It's graphic and intuitive, plus everything fits on one page. The less page-flipping during chargen, the better.