Is there something major I'm missing?
Scope of abilities/skills/powers etc. (There may be more, but scope is definitely an issue to solve.)
For sake of argument, in the simple version, say that Cha covers all the social skills, Dex covers all the sneaking and lockpicking, etc. (I know there are holes there. Work with me, and assume they are handled well enough.

).
Then you layer the skills on top of this as an option. In the traditional model, you've got to divide scope into smaller pieces. This can, of course, be done well enough to get by, if you don't look at it very close. But you will make compromises. The problem is, in such a system, you want
multiple options. And ideally, you want people to pick some options without prerequisites. (A handful may have prerequisites, again for those inevitable compromises, but most of them should not.) If people are going to the trouble to layer complexity on top of a base system, they want to layer their preferred complexity, not yours.
Hero System and GURPs are two ways out of this--but both are built on the idea that the options are all there, and you limit yourself to the ones that matter. There isn't really a "simple" system that is playable by itself. (Actually there is, but it isn't replicated in print--not even in the "lite" versions of both rules. The core is simpler than is printed. There was discussion between Hero 4th and 5th editions of building on this version, and some people suggested that such a Hero would be built on no more than 4 or 5 effects.)
Moreover, if scope is addressed in this way, you radically compromise your ability to convey the mechanics of source material and adventures.
My theory--utterly untested by professional game designers thus far, at least in public

--is that the way out of this is through multiple dimensions of character abilities affecting task or conflict resolution, but
not as derived abilities. It is the derived part that causes the design to either screw up the scope or screw up the math.
For example, go back to Charisma as social again, as base. Instead of skills dividing this up, or feats adding on, or whatever--you always use Charisma for the base roll--no matter how many options you use. If you are using the simple version, then that roll is it--much like skill rolls are now. If you are using skills or feats or both, then those things add
different mechanics that complicate the resolution, but not the roll.
Perhaps skills are focused on addressing sim issues. So if you use the skill option, you are explicitly invoking sim. Skills becomes things you train to do things that not everyone can do, still using your base Cha. "Diplomats" use charisma to negotiate when formal language and protocols are required. Maybe feats are about changing the grounds of the rolls by situation. If you are a "fast talker", you can use Cha rolls faster than normal. (You could just as easily do this the other way around, where the feat "Diplomat" handled special sim cases and the skill Fast Talking modified some situations. It might even be better than the first way, depending on the mechanics.)
In such a model, "races" should be largely replaced by "culture" as a mechanically significant dimension. Being a dwarf doesn't mean much, except perhaps for a few racial benefits that are largely static. Being a dwarf raised under the Granite Mountains, as part of the stonemasons guild, however, exerts some mechanically meaningful heft.
I quite happily admit that this is all mostly theoretical, beyond some practical, mostly failed, home brew system work I've been flirting with for several years now. But I don't see any other way out of the scope issue.
