As I said in another topic, FF X is my favorite in the series, followed by probably FF VI and then FF VII. I just thought that FF X had the best story in the series, as not only is Yuna's story well-told but all her companions actually have stories that complement hers. Yes, Tidus is annoying early on and the game is very linear until near the end, but I found that the trade-off for that linearity is that the story got solid focus. There was little, if any, filler and the game kept a constant momentum. I also find Spira as a world incredibly interesting and beautiful, like it has a history. Pity FF X-2 had to take everything I liked about FF X and chuck it out a window.
I actually prefer the Sci-Fi RPG setting these days, so I'm especially looking forward to FF XIII. After all, just about every other JRPG these days is using the traditional fantasy setting in some form or fashion so it's a good change of pace. I know it's a low bar to clear, but at the very least it can't possibly be worse than FF XII, which had an interesting world that had nothing interesting happen in it.
As for FF IX, GP, I will say this: Zidane is awesome, but he's wasted on that game. It's a solid game, but it just felt incredibly bland to me. Especially after playing FF X, the game world just felt incredibly artificial and contrived like it was assembled from some traditional RPG cookbook. FF IX also suffers from an abundance of useless and/or filler characters, as only Zidane; Dagger; Vivi; and Eiko actually matter in the story. You could cut Quina; Amarant; and Freya out of the story and miss nothing, not that there's much to cut since those 3 are barely even in the game. Granted, FF VI had this problem even worse, but at least that game didn't try and pretend that its extraneous characters mattered. Steiner's amusing, but his one-note gag gets old fast. I also found the plot rather loose and not terribly interesting. It's not a bad game by any means, but it's nothing special either. And after all these years, those PS1-era 3D graphics are ugly as sin (IMO, Chrono Cross is the only good-looking 3D PS1 game, and that game has a host of its own issues).