I'm just gonna throw down the whole order and the worst is the one on the end:
V, III, XI, VII, I, IV, II, IX, XII, X, VIII, XIII, VI
No Obviously I can't get away with just saying VI is the worst and leave it at that, so let me explain - I just couldn't get into the story, which was far simpler than I expected. I also couldn't get myself to care about any of the characters, which is weird for me. I think it has to do with how it all started off, It put me in a cynical mood. Then there's the gameplay, which I found to do too easy and unbalanced; I found myself relying on certain moves and patterns that seemed to be working for nearly every enemy I encountered. I think the biggest problem, though, was the pacing - everything just seemed to happen so fast and it would introduce one bewildering gameplay element after another, most of which would never be seen again. So yeah, that's why I think FFVI is the worst Final Fantasy IMHO.