Look, I'm not here to argue the best Final Fantasy game. Chances are, your favorite is one of the first ones if not the first one that you've played. Unless you played one of the original three first, in which case those hopefully aren't your favorite. Starting with Final Fantasy IV, every entry seems to have its cheerleaders.
As for IX, I was definitely one of the people who originally wrote it off because of the way the characters looked. After loving VII and enjoying VIII, it took me by surprise to say the least. Luckily, my buddy forced me to watch and eventually play it for myself and I realized just how great Final Fantasy IX is. If you enjoy the series but for whatever reason skipped IX, now is the time to remedy that.