In my opinion, there is no FF that is the ultimate best in every category. I would say that:

FFVII has the "best" story and the "best" characters.
FFX-2 has the "best" battle system.
FFIX has the "best" theme. It's actually happy and joyful.
FFX is the traditional FF with the "best" graphics, so far. X-2 and XI aren't traditional FFs and XII isn't out in anywhere but Japan yet.

FFVII would probably be the best if the graphics weren't so sucky and there weren't so many grammar errors in it. An FFVII remake with PS3 graphics, completely fixed dialogue and grammar would probably be the best game the world has ever seen. ._.

And about FFVIII, I think that the junction system is the worst system in all the FFs I've ever played.