I still think the idea of gear granting skills is a valid option.
You start as apprentice level 1--you go and kill the invading gnolls. From the gnolls, you pick up certain pieces of gear..lets say the plate wristguard of smiting. This wrist guard is +6 divine skill, +3 Weapon Skill, and whatever stats there might be along with it (AC, Dex, HP/Mana, etc..)
You now have 6 points to spend in the divine skill tree, 3 to spend in the weapon skill tree. These trees grant skills/upgrades to aspects of that tree. You"d be able to re-arrange your points once an hour, or every time you changed pieces of gear (gear could only be changed outside of combat--would need a check to make sure a different piece of gear was put on rather than unequiped/equiped).
Weapons could either grant more points, or my preference; Weapons would require X ammount of skill points in a tree.
This would allow you to control the ammount of power capable to be gained by a person, while there being constant advancement of character, and customization out the ass.
Lets say you have two "sets" of tank gear--one with a LOT of +defense skill gear but lesser hp/mana/ac, and one with a lot of hp/ac/mana but lesser +defense skill.
Now this allows you to flex your encounters. One encounter against, say, a giant beserker would favor the hp/mana/ac set. Another encounter against a dragon with breath weapons would favor the extra skills of the +defense set--which would be all about different shield blocks of the "big" attacks (breath weapons, tail jabs, etc..).
Then again, I"m just a guy with a (probably bad) idea.