First generation all the way.

Part of the reason is that I personally think that 2D beats 3D anyday of the week. 3D may have more gameplay possibilities, but 2D is better for setting a mood or sense of style. in FFVI the opera scene uses washed out black, yellows, and taned tones to create a old photographic appearence, and also uses muted colours during the performance to establish a melancholy mood. Not to mention the entire sequence was brilliantly directed and the music and lyrics are beautiful beyond description. most artists using 3D graphics and CGI try to overwhelm with funky images instead of just making a emotionally gripping scene, and only a few game designers (like hideo kojima or the team behind ico and shadow of the collossus) can use 3D to equal effect.

Other then that, FFVI's story is just the best, its gameplay is perfect with alot of variety and very epic battles, the music is the best in the series hands down, and all the FF's that came before it are almost as good as well.

2nd generation?

FFVII = alright
FFVIII = WTF
FFIX = hit me baby one more time (in a good way)
FFX = best of the 2nd gen
FFX-2 = WTF were you smoking?

2nd gen has been way too spotty in quality

And I dont consider FFXI to be applicable since its online.