Hm... this requires some thought.

For the boring answer I am going to go with FF2. I unfortunately can't take the game seriously because of it's leveling system, had they gone a bit more conventional it probably could have stuck in the collective FF fan consciousness a little better. But lets move on to an answer with a little more exposition and controversy.

I am going to vote FF13. I consider it equal to FF12 in many respects, but I think it actually has a much better base to build off of.

First off the setting is more conducive to a 'Final Fantasy' game. I am much more concerned about the fate of an entire planet than the succession squabble of a small desert nation, thank you very much.

Secondly the battle system is a lot easier to improve right off the bat. Allow you to modify the default job AI's via a gambit like system? Miles ahead already. The idea of taking your role away from micromanaging abilities to tactical decisions had potential, but the only problem was the tactical options you had available to you were exceedingly simple. It could have been fleshed out (and made speed a lot less important) to add some strategic depth.