So in any case, i think i've identified some of the elements that make each of the middle FFs great, or at least the aspects that one of them was better than the others in. Of course this isn't a "it was mediore except for this bit that was pretty good," it's more of a "wow this game was great, but these particular bits really stood out"
FF4: Epic storyline. Yeah, FF5 and FF6 had pretty epic storylines, but FF4 gave the best presentation of an entire world fighting against destruction, as opposed to most of the world sits around and does nothing while a few people deal with the problem. This is most obvious during the fight against the giant.
FF5: Best. Game system. Ever. Note that the best side game, FF:T, completly ripped off this system :)
FF6: Best music, and most artsy ending. Either FF4 or FF5 gets the best ending period award, still not sure which, but FF6 has a very interesting theme that ties in with the aforementioned great music very well. Unfortunatly sticking to the theme seems to have precluded some of the other usual ending type things, like resolution, which is why it doesn't get the top overall ending award.
So this hasn't actually decided the original question, but i thought it was interesting anyways, oh well.