That's sort of my thinking too - the "skill" ability levels would govern which (as well as how many) of that category's skills you could learn (i.e. bringing back one aspect of the system that had been in prior beta versions, with "Level 1" through "Level 5" skills)
You want to restrict skills levels through ability levels? I don't think we should get back to that - it will yet again encourage players to neglect other abilities and invest points only into Way of the... abilities to get most powerful skills asap. I think new mechanics are better, restricting only the amount of skills. However I agree that Way of the... abilitites need more bonuses with each level.