3. Final Fantasy XII
This system, for the first time in the series' 20-year history, really blew things wide open. Yes, the battle system goes through evolutions for every sequel. But this radical re-imagination took the button-pressing out of fighting with its associated and crucial Gambit system, which allows players to craft complex behavior that the characters will follow unflinchingly. The whole thing is strangely liberating, if a bit-hands off for some. It deserves kudos just for being willing to throw the rulebook out and truly re-imagine what an RPG battle can be... even if it's not exactly as much fun as some of Final Fantasy 's other attempts.
2. Final Fantasy IV
This is where things really changed for RPGs. In 1991, Square decided to introduce a realtime element to its already-popular series' battle system. Taking the pure, paced, turn-based monster slappin' of the original NES games in a new direction, these battles were an entirely new concept to console gamers: each combatant, friend and foe alike, was judged and acted in the order of his or her speed, ensuring a constant back-and-forth. The battles were much speedier and more engrossing than anything that had come before, and with a party filled with unique characters with creative special abilities, it only got more fun. A landmark moment for the series, no doubt.