At least three things spring out immediately to me as criminally under-served as skills.
The movement subsystem.
Tumble, athletics, climb, jump, swim, balance, maybe even escape artist or endurance. Going cross country, flitting across rooftops, squeezing through sewers.
Some of these are just reflex saves: a balance check to stay on a high and windy ledge and a reflex save against a pit-trap are not so different!
Some of these are clunky as a skill check, but fine as an ability, like tumbling around foes in melee.
And some are special modes of movement that a character should be able to specialize in, but skills aren’t imaginative enough: shouldn’t training in climbing make one more at home on the wall, faster, and more stable, in addition to merely surer?
These should be straight attribute checks with the equivalent of feats to grant improvement.
And a really obvious “feat” just removes the need to roll in some set of common cases, or ignores some category of difficulties (climbing without tools? That’s fine, you’re trained, common tools don’t help you anyway!)
The social subsystem.
Diplomacy, intimidate, deceit/bluff, sense motive.
Oddly, nothing to taunt, bribe or seduce; I find those pretty typical PC approaches to problems.
This one is just limiting. Your character with a massive diplomacy: once upon a time, that would have been a massive charisma bonus. It’s encouraging paying for something twice, once in stat and once in skill. Boo!
And then we get to Bluff/Deceit: I’m very convincing, but only when lying? Or maybe even then, but then whither diplomacy? Feh.
Trash the whole thing. Make each of these skills into maneuvers in some social skill-challengy thing. Heck, play a hand of poker, then modify results by charisma mods, it’s just as reasonable as the rules.
I think that the big problem here is that people are complicated but skill checks aren’t. Pass-the-duke-is-convinced, fail-he-isn’t. Not enough granularity in outcome.
Maybe something like having every character rated for the four humors, having characters able to influence which humor dominates, and every interaction modifying future layouts.
Something like Trust, Greed, Fear and Obligation.
I haven’t really thought about this 🙂