Probably the best solution is to have both skill points and Stats increase skill damage. Something like Energy could increase the effectiveness of Magic Missile, Strength for weapon damage and thus Cleave by extension, Dexterity for inevitable bow attacks. This also means there would be some increase each level with auto-stats.
How ever, the progression through stats alone will be slower than with points. Thus while all skill would receive some scaling, and more so if you increased stats through items, it would mean the player couldn't just put one point into a skill and expect it to be useful 20 levels later.
Q u o t e: Assume that whatever Grug says I agree with, so any loner he's arguing with instantly loses 2 to 1. -Cpslostudent