Only topped by Terranigma for me (absolutely personal opinion, not saying that it is better or not), might be because I played Terranigma first and the desolate World that you revive appealed to me more at the time. Still, when I first played CT I was blown away, from the visuals to the OST (best OST of any game) to the characters, it was perfect. Never played another game that could take that 2nd spot it holds in my list.
The short lenght of both might have something to do with it as well, they tell what they have to tell and don't overstay their welcome. Terranigma's ending did stay within my thoughts for longer though, my little heart was left broken.
Really makes me happy that people still discover this game today and enjoy it so much, it's a game that deserves all the praise it has and then I get sad that I never see these LTTP threads about Terranigma, I truly believe it to be very underrated.
Anyway, sucks for you OP, you won't play another JRPG that will top this, you made it, you reached the top.