IX is near the bottom of my own personal list after you account for the usual bottom tier mainline entries (13, 15, 2, etc.) for a few reasons:
1) I'm not a giant fan of most of the cast, namely Quina, Eiko and Zidane. Zidane just came off as creepy to me and Eiko just felt like they could have given all her skills and abilities to Garnet and lost nothing. I like the concept of Quina but did not like the eating for blue magic aspect.
2) The game gets horribly boring in a few places, most notably the Gargan Roo which always puts me to sleep at least once on every playthrough. Final Fantasy 9 is the only FF game I've ever played (aside from 11 for different reasons) that I've actually fallen asleep playing multiple times. I feel like a lot of the stops the party makes drag on and on.
3) I really am not a giant fan of Kuja after 5, 6, 7, and 8's villains casts.
4) Not a fan of the way you learn skills at all when compared to 5/6/7/8.
5) The card game in FF9 sucks compared to 8.
6) I didn't find Ozma a very compelling or interesting super boss in comparison to 5/7/8 especially.
There was plenty I did love in the game though!
All in all: I think FF9 is a fantastic game (I like all the Final Fantasy mainline games to a certain degree) but it's not in my top 5 mainline games and may not even be in my top 10 if I was ranking only 1-15. I still play it (and the rest of the franchise) yearly.