I divide this into to categories, in battle and before battle setup:
Battle Setup:
FFVII gets the cigar for me, it was abusable but I love to have customization control over my characters.
FFVIII gets second as the junction gave a lot of customization control and a much more in depth system.
FFX, the spheregrid was enjoyable though I wish I had international so I could customize my characters better.
FFIX had a very well done abilities equipping system.
FFT was also pretty good for this.
No other FF had a very good battle setup system, I'd probably go: FFV, FFVI, FFIV, FFI

In Battle
FFT utilized the strategy rpg system beautifully, it would have been nice if more strategy had been involved though like in Vandal Hearts.
FFVIII/X-2 These games both show the ATB system near it's best. FFX-2 allows everything to occur at once and FFVIII has the perfect timing between every turn to really make fights enjoyable.
FFX performed the wait system excellently.
FFV had an extensive job system allowing for very different parties to use in combat.
After this the games aren't as strong but the order would go FFIX, FFVII, FFI, FFIV, FFVI