I really liked the example or direction for skills and stat usage that I read in a another post some-where on this board, with my own personal twist...
Category (tier 1) - A grouping of similar or like skills (Stealth, Martial Combat, Woodcraft, etc). No stats drive a category, but character classes / professions would provide a bonus to learning and using skills. # of ranks in a category is equal to the sum of all skill ranks in the category (this would likely mean a revision to category bonus progression as the number of ranks would be much higher).
Skills (tier 2) - The actual skills (Stalk, Hide, Pick-Pocket, etc.) 2 stats anchor each skill and the character invests development points to 'learn' or develop more proficiency with an individual skill.
Usage Modifiers (tier 3) - Usage modifier aligned with stats. Use Memory to remember Lore about a skill, use Agility, Strength or Quickness to perform some of the skill manuevers, use Reasoning to learn new concepts of the skill or category, etc.
So, a simple example is that the player wants the character to be good at the Stealth Category of skills. He develops a thief arch-type with a +10 bonus to the Stealth Category (this applies to all Stealth skills), he develops 3 Skill ranks in Stalking, 2 skill ranks in Hiding, and 3 skill ranks in Lock-Picking. This makes him have 8 ranks in the Stealth Category (which provides a bonus to all skills in it), which helps to associate concepts of a skill in a category to other skills in the category in my opinion. Then, the action specific modifier is applied by the GM for an action request from the player.
"I want to try to remember all I can about 7 tumbler locks"..."Okay roll Lock-Picking + Memory" translates into
Category (Profession Bonus plus bonus of all the sum of all skill ranks in the category)
2 pts per rank from 1 to 10
1 pt per rank from 11 to 20
1/2 pt per rank from 31 to 50
Skill (2 stat bonuses plus developed skill rank bonus)
3 pts per rank from 1 to 10
2 pts per rank from 11 to 20
1 pt per rank from 31 to 50
Action Modifier is the addition of the Stat bonus.
Those are just examples, and I haven't thought it all the way out, but that's what I'd like to see.