I might take things in a simpler direction, with the same basic aim. We could simply take 3E's skill system and cap all skills -- and quasi-skills, I suppose, like BAB, Saves, etc. -- at 10 ranks.
Once a character has 10 ranks in a skill -- or quasi-skill -- any additional skill points or bonuses get spent on other skills. (I'd also kill the double-cost on cross-class skills.)
That works for ranks, but what about base attack bonus advancement? If you think that a +20 bonus is a bit much for any character, as I do, then you still haven't solved the problem. I think that skill advancement in itself isn't the real culprit in higher level play difficulties, but rather the steady +5% per level across the board advancements.
I never found d% system to be really use it. You rarely use the fine granularity it provides.
I think this is more of a game design issue. The level of granularity would be imposed upon the player if the design is any good. The real trick would be to keep things from being significantly more complicated than what D&D currently uses.
And if slow down advancement, the whole "fun" of leveling is gone, since it only grants you diminishing returns. You should be prepared to give players a new toy at that point.
I disagree with that for the simple fact that you would still get to play your character. Out of the people I know who game, most of them abandon the characters once they hit about level 15 because after that point it becomes difficult to manage the game. There are too many options available to the player, too many spells to pick from, too high of BAB differences between characters. Frankly, I've never run a campaign that high myself, but those who do tell me that the whole CR system breaks down at that level.
You can keep power levels under control without making leveling less fun. Any bump in the BAB progression would still be a bump and a goal worth working towards. Any new abilities, new skills, etc. are still increases.
Another strategy would be to do the static increase that you see in D&D, but make the progression a +3% increase rather than +5%. You would still end up at about the same place by level 20, which is +60%, the difference being that the increases were uniform throughout character advances, so leveling would still seem to be more significant at higher levels. The drawback is that you would still be at +90% at 30 levels, so the game would still eventually get to the same difficult to manage point - unless you cap certain things at level 20, in which case we still have the same scenario as before with diminishing returns - they're just postponed.
Ultimately, most groups have to make the choice of power caps or ending their campaigns because most of the most committed DMs just aren't willing to keep going into the upper levels.
At least that's my experience with 3rd edition. Based on what I've seen of 4th, it's going to have less of a problem with too many options/bonuses, but it will still have the same problem with the never ending power increases. I'd like to see what people who are playing a high level 4th edition game think, but I suspect that the problem hasn't completely gone away.