I've been pondering the issue of capstones. In the old system, capstones were a reward for staying 'pure' but they were inconsistent in their usefulness.
I think in the new system, capstones should be divided into two categories: prestige capstones (for spending enough points in a tree) and class capstones (for reaching 20 in a class.) Prestige capstones would require a point expenditure in their given tree, and would be exclusive (meaning if you have a prestige capstone, all other prestige capstones are locked out, unless specifically excluded for in the capstone's description.) Class capstones would be naturally exclusive, due to the requirement of 20 levels in the given class, and would cost 1 AP. A 20th level fighter/kensai could have a prestige and a class capstone, as a reward for focusing on a single class.
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Upon reflection though, the class capstone idea might need a little tweaking. Just like there are different element focuses for sorcerers, there are also different weapon focuses for melee classes. Perhaps there could be 3 or more different capstones for each class, each exclusive and locking out the others, which give the character the desired power.
An example for that would be a ranged Kensai fighter 20th level. Her class capstone might have ranged alacrity 15% or 10% doubleshot. A dual wielding 20th level kensai fighter might choose 10% offhand proc chance or melee alacrity 15%. A two handed kensai fighter might choose a capstone which doubles STR damage on two handed weapons, or adds a 15% chance for weapon proc off glancing blows.
What I'm trying to say is give the players a swath of options. If you want the new system to be popular, people need a veritable buffet of choices. If you limit them to one or two, you will hamstring your efforts to improve the game.
I REPEAT: Balanced variety is the key to this pass being effective. If you keep things too simple, sure it will be easy to implement, but it will leave people wanting. If you give people a lot of choices, you will make more people happy.