I didn't play either of these games on the SNES. Instead I played them both for the first time in the 21st century. FFVI I played on a PS1 disk, and I enjoyed it a ton. It's an extremely good game, and it might have become my favorite RPG ever if I had played it when it was first released. Chrono Trigger I played on the DS and couldn't finish it. Although to be fair I have since realized that I really need to play RPGs on a big screen to really enjoy them. At some point I'm going to play Chrono Trigger again sometime on a bigger screen and see how I like it.
So, for me it is very much FFVI that is the better game, but I may change my mind about Chrono Trigger once I replay it.