Out of main series offline alone (because else XI and XIV will dominate the list), my top 5 (in no order) is V, VI, VIII, X, and XIII (a guilty pleasure, caused by the game actually being challenging).
The problems I have with FF9 are just vast. Minigames (except Chocobo Hot and Cold and the Impress Nobles one at the beginning) basically just exist and serve no purpose, not even a real reward for really doing them. Tetra Master has a hidden RNG element that betrays the numerical stats and destroys all enjoyment of it. Half the cast gets no character development and the story goes off the rails once Disc 3 hits. The entire final area alone (this one I'm sure everybody has issues with). Battles take double the time of battles in other FF games due to how slow the animations and ATB are in this one. Trance is basically just a poor man's limit break that can't even be controlled or considered too useful in most circumstances. I could keep going on and on, but you're getting my long list of complaints.
That's not to say there aren't some things I really do enjoy, because what the game gets right, it gets right really well. Chocobo Hot and Cold is legit fun, and always stays relevant due to the rewards and treasure maps giving you high powered gear often before you're really supposed to get it. Synthesis shops guarantee that all pieces of gear are useful at some point, as does learning abilities from them. The world itself has one hell of a Studio Ghibli type vibe that just makes you enjoy the world and designs, with no area really looking similar to another. The few characters the game actively gives character development to are my favorites in the game because of that development (Zidane, Dagger, Steiner, and Vivi). But none of that can really override the amount of problems the game has. If that rumor of a remake is true, I hope they fix most of this so the game is redeemed to me, like how Zodiac Age redeemed FFXII.
Didn't like Dissidia NT due to how...bad it was set up. Loved the hell out of the original Dissidia, as well as Dissidia Duodecim. Opera Omnia I rather enjoy as well. And World of Final Fantasy I really liked because of how the combat was incredibly strategic, along with the twins being fun characters. Not to mention how dark the game actually gets. Took a bit to get used to the chibi style though.