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 ).
Nothing else reaches the same quality as Chrono Trigger in the same way. You have to settle for lower quality with similar pacing, or try to reach the same level of quality in a different way.
Similar pacing, lower quality: Phantasy Star IV, Super Mario RPG, Final Fantasy IV
Comparable quality, different style: Earthbound, Final Fantasy VII (FF6 is the real answer, but FF7 is the most similar game to FF6)
Similar aspects, lower quality: Dragon Quest IV, Radical Dreamers & Chrono Cross, possibly Radiant Historia
Radiant Historia definitely hits some of the same notes.