Never played the S/NES releases or XII. Really need to get around to doing that (after I play through Shin Megami Tensei, Live-a-Live, and so much else...)
Anyway, my preferences:
IX>VII>X=XIII
Rating X and XIII just about even. Neither had particularly good plots, but XIII had an intriguing combat system and X was far better at hiding its strings. Every other flaw or positive note about either game has a corresponding one in the other (both have awful male characters, for instance). To be honest, I'd put Tactics on the level of FFIX (if not higher) if I didn't consider it cheating. Too different from the main series.
For the record, FFVII isn't overrated. All the media surrounding that game and setting have indubitably soured people on Cloud and the gang, but if you look at the game and the game only, it's nearly perfect. What people seem to forget about it is that it was every bit as comical and cheery as the other installments. Sure, there are some dark and/or unnecessarily melodramatic and overbearing moments, but it's hardly "emo" the whole way like XIII was[footnote]Not entirely accurate, but it had some awful pacing and no good relief. Even VIII had some comic interludes and the occasional charming character, despite being largely terrible...[/footnote].
Instead, it's fairly inventive fantasy (no orcs/undead/orcs with funny names) told in a steampunk setting with some minor sci-fi elements. While the combat is old hat now, I remember having loads of fun with it back in the day. [small]Also, Tifa[/small].
But IX is still better. That's not a point against VII, IX is better than a great deal of things. It's just so damned charming. Everything in the game is beautifully crafted to deliver a simple story with a surprising amount of depth and care. Even when extremely common RPG tropes materialized, they fleshed it out enough and played it confidently enough for it to work.
Granted, the character designs are a little weird. Not bad, just weird. Fortunately, the graphics had advanced to a point where the 3D models didn't look (as) ridiculous anymore.
[sub]I also don't get the hate for characters like Yuffie or Quina. They're festive! They're not as silly as Vincent! Phoenix Down cures KO, not death![/sub]