yeah it came out at a bad time, which is unfortunate. Seems to happen with a lot games (I remember a lot of late SNES rpgs got looked over cause people were already thinking Playstation). I think IX actually came out AFTER PS2, cause I kind of remember playing it on PS2.
I always kind of hoped IX would develop some kind of cult following, but it never really happened. Funny thing is, it's actually the highest rated of the FF games on gamerankings.com... granted, by a VERY marginal amount, but I think a lot of people think of it as a throw-away kind of (maybe because it wasn't even supposed to be in the main series) but that's clearly not the case.
I was reading an article about it not that long ago that basically said the lack of interest in the game was a combination of bad timing and also too much borrowed from previous games. Basically, younger gamers were already busy with their PS2, but the game didn't feel "fresh" enough for older Final Fantasy fans to care about. Personally, I think that's crap, because with the exception of Kuja's antics, the game doesn't feel like a retread whatsoever. And even though Kuja's story and plan was reminiscent of Golbez and Kefka, his character was very different, as was the dynamic between him and the heroes.