For me, I personally would give the game a total overhaul. First would be some more links to Chrono Trigger, as CC feels like a 3rd party game with some last minute translated words to link it to CT just to ride on its coat tails and sell some more copies.
The amount of playable characters, of course, too high. Their speeches seem canned at times, its like whoever wrote CT wrote out scripts on the basis of X event with Y character, whereas CC felt like they tossed in "good job person" all the time. You couldn't have a proper character interaction based on who you had...there would be ten thousand scripts. Think of the permutations!
And critically, cohesion. Not just with CT but with itself. There's so much left unknown, the only link to this game really was Radical Dreamers, its more like CC was a sequel to it and yet no one played it outside japan (and RD itself I found tedious, I finished it soley caise i love CT). Somewhere in the studio someone wrote a whole universe story and used most of it for CC. thats the feeling i get. like how futurama had the whole timeline theorized before making an episode. I feel like the guy who had the final say in CC looked at the WHOLE chronoverse and approved off on CC, leaving out one or two facts on the basis "it makes sense" yet WE didnt see it all so it doesnt make sense to us. Were you holding out for one more sequel? If so, make it! Kato, help us out here!