Well, I like FF6, but comparing it to Chrono is like comparing apples to hime-sama. As for the points brought up...
POINT 1: Random encounters vs. triggered encounters.
Well, I personally prefer the Chrono system in this case, but there is a time-tested solution to not fighting battles you don't want to fight - it's called the L and R buttons. Works in both games. Also, Sora, moogle charm isn't available until two thirds of the way through the game, which makes that kind of pointless to those who probably haven't gotten out of Magitek Factory yet.
POINT 2: Graphics.
I don't judge based on graphics. Leave this to someone who cares.
POINT 3: Character design
I take issue with both your views here. Yes, Crono IS cool, but to say it's because of looking like Goku...that's no point at all. Toriyama's character designs aren't very varied. He's got more Goku look-alikes than you can shake a power pole at. As for Sora's digression on Kefka v. Lavos: What. The. Hell! First off, Kefka was hardly the first villain to start small and become godlike. The name you yourself brought up, Chaos, did the same thing. Second, Lavos just a random end boss?! It's built up throughout the game as an unstoppable force, its influence is felt from the halls of Zeal to the ruins of the future, it freakin' KILLS CRONO, and even after it's annihilated, it just gets more dangerous! That's no random "big stupid monster", not at all!
This said, I also love Kefka as a villain, but he's an entirely different kind of villain.
POINT 4: Music
Both soundtracks are godly. I'd say that out of battle, edge FF6, in battle, edge CT, except for Dancing Mad, which is, well, Dancing Mad.
POINT 5: Engine
Seconding Zeal here - while they are both 2D RPGs with 3D effects from Square, the engines are NOT the same. Field engine is different, battle engine is different, graphics engine is different.
Finally, comparing debate to sexual violation? That's rude, wrong, and probably grounds for the law of the land to come into play. Bye-bye, kid.