Hmm, again, I seriously don't see a way to count that last monster as being killed. So any system that works on their "normal" way of assigning AP (per monster instead of per battle) won't work properly.

The only other thing I can think of would be to make AP an extenstion of EXP - that is, if you earn 1050 EXP in a battle, you'll earn (1050 / 100 ~= 10) AP. This wouldn't be too hard, you'd just have to check the difference in your EXP from battle to battle. However, the system has the disadvantage of requiring large amounts of EXP to earn any reasonable about of AP, and you couldn't set it from monster to monster unless that battle disables escaping.