Not an FF, but still made by Square.

Drumroll

Xenogears.

Because I'll see your Espers/Summons/Doll like black mages and raise you one giant robot designed to slay God itself. Hands down the most engaging and story driven game Square has ever made, a true masterpiece. As far as FF's go, IV (Or II for SNES) was also an epic title. Kain is and always will be my favorite FF character. Tactics was also a masterpiece, because Delita was such a unique character, I only wish he was playable!