From one perspective, it's no doubt FFIX because it's really the only game in the series that didn't improve on what came before it. They basically just used the VIII engine. They could have at least programmed it in a way to have faster load times. The series as a whole has alot of merit for doing something different with each title, so for a game to be made relying solely on the previous titles, creatively and technically, that's a huge loss. Not to mention how cheesy the entire plot was.

But IX is undoubtedly one of my favorite games, not just in FF. Now I have to give a preamble to this - while I don't dislike any FF, VI seems to be the one that does the least for me. About halfway through, or sometimes in the WoR, I really have to convince myself to continue playing it. Which is a shame because I do usually enjoy solving each dungeon in that game.