Left feeling a bit empty after playing it for the first time a few months ago(why did I wait so long?) I am afraid no JRPG will be able to surpass it. Would love to have a discussion about similar games that reach the same quality level (Note: I have already played Final Fantasy VI ).
I liked Golden Sun and Golden Sun: The Lost Age more than Chrono Trigger.
Super Mario RPG is pretty high up there, as well.
Lost Odyssey is a gem that doesn't get enough love. Chrono Trigger might be a bit higher on my list, by this is definitely worth a playthrough. Be prepared for some real pulls at your heart strings if you read through the short stories in the game.