Writing, easily. The story's fun, but I think it has too many weak elements--Garland, Gaia and Terra, Kuja and Necron--to be truly great. It's just that the general character development, atmosphere, dialogue, and everything else put into the game elevates that story into something really wonderful. The localization deftly mixes goofiness and high adventure and charm so well, and the ATEs are a really cool technique for expanding the narrative.
I love basically everything about IX, but the writing's so much better than most other Japanese games of the time it's really incredib