Disproportionately punish melee classes? But that's why you put points into strength and constitution. If anything, if your mage ends up getting knocked down and you didn't put any points in constitution, then he's probably fucked. The setup I was talking about makes all of the stats have some sort of affect on everything to do with AP, with the exception of Perception.
So, Warriors, naturally should have a high strength and constitution. So, they would put points into that, allowing them to take on the front line challenges, while a mage wouldn't be able to do that.
The way I explained it was so that warriors are warriors and mages can't just naturally be warriors. So, while your mage might be able to wield a 2handed sword, he won't be able to use it as effectively as a someone with a higher strength, damage capabilities and bonuses aside. But he could still use it if he really wanted to. But say he wanted to don some heavy armor, he's not going to be able to wear it as well as someone with higher strength than he has, so he won't regenerate as much AP due to fatigue.
I don't see this punishing anyone other than the people who focus everything in one stat. This diversifies what you'd need to keep going.
This isn't a 'add this on', this is an entire rethinking of the AP system.