Chrono Trigger, in every way.
FFVI is lovely. I know they're both JRPGs, but it's almost apples to oranges. I really like the atmosphere and story of FFVI, but I love that in CT too, in a totally different way. But in the end, Chrono Trigger wins in story, characters and especially gameplay. The battle system of CT is what introduced me to RPGs. FFVI is great too, but CT's gameplay structure was the first in the genre where I got a real sense of fun. FFVI battles were rewarding, but playing CT is both rewarding and fun at the same time.
So it's CT for me.