MvC2, you dastardly bastard. That's like asking me to choose either water or air. I think I'd have to give the edge to FFVI, but we are talking a 1% margin here.
One thing FFVI has over Chrono Trigger for sure is the soundtrack. Don't get me wrong, I love Chrono's OST which has a lot of catchy tunes. FFVI's however has one of the most emotionally charged soundtracks I can think of. Celes' Theme, Terra's Theme, Forever Rachel, Searching for Friends... the list goes on with so brilliant mood setting tunes. The more I think about it the game just has so much more emotional resonance in it's story which I am likely associating with the music.
Chrono Trigger has a more original story overall, but FFVI has a much more personal, character-driven one. Chrono for sure has this too (Post-Lavos future, Frog & Magus, etc.) but in FFVI you get this kind of thing from nearly every character. That is my preference in story telling, I guess.
I like FFVI's combat more overall as well. Chrono's combos are cool. but all the characters of FFVI having unique abilities that vary wildly as well as being able to customize them with the magicite later down the line makes it come out on top. Both games are an embarrassment of riches in content so it makes me feel like a bit of a dick FFVI has slightly more. Of course, Chrono's multiple endings do well in making up for this.
Overall, both are exceptional games but FFVI is an exceptional game+. We're talking a 95 A vs. a 97 A+ here, so not that much more but just a pinch of extra spice.
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Also... unrelated thing that's bothered me for years...
I swear there was a time you fought Lavos while the main Chrono Trigger theme played but I can't find any video of that... did I just make that up out of faulty memory...?