Crossword pretty much hit the nail on the head as to why FFIX isn't very well liked in some circles. Then there is the whole Kuja issue.. I still remember how pissed some people were when they found out Kuja was a guy.. T'was entertaining to watch them bitch about it to say the least, though it's another reason why some people don't like the game. (As silly as it seems.)
Really though, I found FFIX to be one of the better ones in the series.