I liked FFIX a lot as well. I like to think of FFIX as a return to the old days of Final Fantasy (I mean, it really was). In particular, I liked that the characters had set classes, as opposed to the open-ended roles the chars in FFVII and FFVIII had. In those games, the only big differences between Cloud and Cait Sith, and Squall and Selphie, were stuff like the weapons they used and the Limit Breaks that were unique to them.
But in FFIX, the chars had a specific class-type build (the main char is a thief-type, meaning he uses daggers and has high speed, but can't wear heavy armor and lacks magical prowess). This made it so if you needed black magic, or if you needed a physical powerhouse, there was only one character to turn to for each.
Aside from that, I liked the fact that I couldn't get severely powerful at any point in the game, whereas with FFVIII and its Junction System, I would do 7000 damage with a triggered hit with Squall after becoming a SeeD (not even midway through the first disc >.>). FFX had a similar problem with the Sphere Grid...
Final Fantasy really needs to stop holding the player's hand through the gameplay. XD So much focus on storyline and graphics, when the game mechanics and battle system needs to be improved on so much~