FFIX had more involved characters, beautiful locals and one of the best storylines in the series. It's music was brilliant, and the writing is excellent, especially considering it's in the PS1 era.

XII is pretty and has better combat. A good game, but FFIX is simply unreal. Oh, and Zidane is a much better protaginist than Vaan. In fact, I find only Terra and maybe Cecil to be better. Since Zidane matures rather than changes, at the end of the game, he is wiser and older, but still has the same personality unlike say, Squall or Cloud.