Honestly, I can't really put my finger on which one I like the most, or which one I feel is the best for that matter. I'm a little inclined to discount FFIX because it didn't take many risks, at least not relative to FFVII and VIII. But that's a little arbitrary since its merits as a game stand just as strong if not stronger in some areas.

A big part of these games are the art and music, and for that it will always be extremely subjective. It makes it even harder since they were using essentially the art presentation/implementation design and the same sound tech, although I would say VIII and IX were quite a few levels up from VII as far as sound quality goes.

On battles, I think VIII had the best character development system, VII had the best flow/direction of ATB and camera, but IX's was the most well rounded, and probably the most polished by far. However, I really dislike that FFVIII started, and IX followed, the tradition of only having 3 monsters on the screen at most. This continued in FFX and was retroactively implemented in FFIII DS. You could argue whether or not having more than 3 potential monsters increases or decreases strategy, but I think I prefer more than 3.

On story it's hard to say. VII implemented various techniques and influences and felt really original to me. It had the most actual themes out of the three. VIII was highly emotional and very realistic, it's like a novel almost to me. IX was probably the best put together. It made the most sense. It was able to maintain and thrive with many characters, plot threads, and locations, and just had this great storybook, mystical feel to it.

My opinion has always been that IX is possibly the most well rounded game in the series, but VII and VIII were very much experiments with the RPG medium. I honestly can't decide!