FF6 was my favorite. It has better gameplay and storyline than FF7, which was probably because of Square's emphasis on graphics. I really liked the story of FF8, but the gameplay is broken.
Simply put, after the SNES era was over, I wanted more out of my RPG gameplay. FF10 was not bad, but FF12 just sucked. I own the game, but stopped playing it half-way through. It is just another "healfest" and you would think Square Enix would be able to match the gameplay of Baldur's Gate but they haven't.