I think why many didn't like IX was because it was too similar to the earlier greats that appeared on the SNES. It didn't have OMG cities and big robots! FTW! lol ..or, for rabid fanboys, a cross dressing, spikey haired hero who chased after men, ahem.
But seriously, I enjoyed FFIX out of all installments in the series.. mainly because of the old school feel that was a kin to FFVI and IV. I, for one, also appreciated the art style it used. It didn't swap back and forth between adult looking characters to Popeye-midgets.. plus it had a great artistic flair and design to it.
Then there's the epic rags to riches story, cliche, but awesome.. paired with memorable characters, it was quite amazing, I thought.
Gameplay was classic, pulled right from the great FFVI and there was so much classic things cameo'd within IX that it made it all the more nostalgic, somehow.. while being completely fresh.
I don't know, I guess I just enjoy titles like FFVI, IX and XII more than VII, VIII and X.. which were great, but mediocre compared to the former. Just my opinion, though.
I loved how IX mixed the new with the retro, though.