I'd love to see the Moombas come back, I also liked having the control of Critical hits with Squall's gunblade, maybe more interactive elements in combat to make battles more engaging.

I want Zidane's thief skills, the thief is an okay class unless they give them some BS stats and weapons like Locke and Zidane but I genuinely loved Zidane's thief skills, especially "What's That?!" and his ability to see what item an enemy is carrying, makes stealing way more efficient.

I actually like the Mark system from XII, but I want it presented like XII did it (from the beginning and goes through the whole game, not this last minute quest crap FFX and XIII) but I would scale it down and just make it one of many quests/side missions and not the only major one in the game. It would be easy to attach story segments to these types of quest, to flesh out the cast or introduce optional locations.

More team up abilities, Palom and Porom had it going and its sad we had to wait five games later to get Magic Sword in FFIX. It doesn't have to be as extensive as Chrono Trigger's or Suikoden's systems but just getting a few perks from having certain party combinations is a fun mechanic very few games really utilize.