Obviously there's a lot of elements that come into play as to what makes a game good, when you remove all developer constrictions at the time. FFVI had amazing dungeons. FFV's difficulty scaled wonderfully along with the story to present a consistent challenge. And I always liked how FFII let me build any kind of character I want.

But as VeloZer0 hinted, there's a lot of intangibles at play, and that's why I'd still give it up to Final Fantasy VII. I think it has the best pacing in the series, the best music, and the most cinematic combat of the games which tried it. It's the apotheosis of the virtues of the game designer and his/her ability to craft an experience, rather than leaving it up to the player to make their own fun. Very close is Final Fantasy XII, which was a giant of gameplay and a giant in story.