I replayed Chrono Trigger recently and I should say it still holds the title of the best 16 bit JRPG, for me at least. And I played almost all of them.
To compare CT to anything using solely combatfaggotry criteria is just ain't right. Combat is there to give you sense of progression, you bump into things, they die, nothing to talk about. CT has an engaging storyline about time travel. Who wouldn't like that? It doesn't tire out player with random encounters, senseless dungeons, hardcoretacticalbullshit fights, long combat animations, doesn't overly long, doesn't require grinding (pretty much it has nothing that turns most of JRPGs into painful slog) has pretty graphix, memorable characters, diverse locations, sidequests, nonlinearity, interesting plot, nu game+. It really was ahead of its time, basically, it feels like a mainstream product having high production values, doing everything to keep player engaged. And I did not have SNES as a kid mind you, so no pink tint here.
For me top5 16bit JRPGS would look like this:
1.Chrono Trigger
2.Tales of Phantasia
3.Phantasy Star4 (despite that SNES and Genesis are not in the same league concerning graphics and sound quality)
4.Star Ocean
5.Lufia2(or FF6 haven't decided).
And i refrain from inclusion of tactical/chesslike JRPGs.
So to speak, also replayed Shining Force2 for nostalgical reasons and it is just the case of severe pink glasses. It basically doesn't have anything except too long and tedious tactical battles. Story, equipment, character progression, dialogs, graphics, music, basically everything is far inferior to most of SNES' JRPGs. But again, if combat is your life, maybe there's something worthwhile.