I think FF6, hands down. I think it's Square's greatest masterpiece... amazingly deep and detailed world, both pre and post apocalyptic. I loved the characters, and it was very rare in that there's no main character at all, there are quite a few playable characters, but they're all developed. Terra, Celes, Locke, Edgar, Cyan, and much more... they all get their chance to shine at different times throughout the game. Graphics, special effects, and battle system definitely go to CT, it was so much FUN and great to play or even watch... But for me, the music and artistic style of FF6 (it was a beautifully designed game, even if the graphics weren't as good as CT) outclass CT, and the plot does as well. And then the villain, Kefka was probably one of the most evil villains in a video game. Constantly deceiving and betraying and killing anyone who got in his way on his climb to the top. Plus he was just plain psychotic.
I also think age makes a difference in this vote... if I was a few years younger I wouldn't have appreciated FF6 at the time it came out and probably would have liked CT more. I know amongst my friends, those of us in the 20something age group prefer FF6, while those 20 and under would go for CT.