I did always quite like IX's ATE system as it really helped Character Development away from the main course of the game which was something rather new.
Also - I was rather fond of X's Sphere Grid system as it made people "eventually" interchangable in terms of abilities which was always fun.I think I liked X-2's Mission System but not as much as the Dress Sphere thingy - that was rather inventive I thought but still not as good as IX and X's features.
So overall it's between those two; but in terms of the poll I think I may put the ATE system.