Having played most FF's (FF2, FF3, FF5, FF6, FF7, FF8, FF9, FFX, FFX-2, FFXII) I have the rights to share my unbiased opinion which I think is the best amongst those that I have played through.
For me best overall in terms of story is FF6 (FF3 in the US), this is my very first FF experience but the story is very well done that I give my hats off to such a classic game. This is the only rpg I can think of which hasn't focused too much on a single main character, although I guess Terra is the main antagonist but most of the characters are well developed that you can say there is no main character.
Best in gameplay would have to be FF7 followed by FF6, the only reason why FF6 is not top is that there are major glitches that degraded the gameplay value. I enjoyed FF7's materia system and the challenge it had to offer, I played that game 7 times back when it first came out, I absolutely loved it.
Now I'd like to share my thoughts on the other games and why they failed to deliver:
FF2: I didn't actually finish this game, its too old school simple and the difficulty is insane which is good for hardcore players I guess.
FF5: Same as FF2, too simple and insane difficulty.
FF8: I hated this game only because of its gameplay, draw is so stupid (cast magic and your stats go down, nice concept.... yeah right), hero potion is stupid, on top of that we have..... Laguna card!
FF9: Oh I loved FF9 but its not very challenging, where are the secret bosses? Don't mention ozma because he is a joke.
FFX: I loved FFX and FFX-2's love story, I guess I have a soft spot for romance but yeah it was cool. Still I cannot say this is the best in terms of story and gameplay, I hated that sphere grid.
FFXII: I didn't get to finish this one, it got pretty boring in the long run. I guess I just can't play as much as before anymore, can't spend too much time playing games. But I did like it, it wasn't very original or catchy but it was ok.
End of story.