I don't have a problem with CC as a sequel to Trigger, and I think it's actually interesting in that way. But just having replayed the game, I can't help but feel that the game is the poster child for unnecessarily convoluted. Some games use complex (or even convoluted) to feature exciting adventures with fun developments along the way. But CC isn't really that. Completing the game always leaves me feeling like "what, that's it," because it's the sort of game where the player isn't really aware of what's going on and is always moving to the next point to figure that out. But once you go back and recount what actually happened in Serge's adventure, well, there's not much there after Fort Dragonia. At times it feels like a late 80s, early 90s JRPG, with a lot of inconsequential barriers and diversions. Terra Tower is really the culmination of the writing's problems. It just feels more like random happenstance than anything impressive or exciting. There is the story about the war between Chronopolis and Terra Tower, but guess what, that's not in this game. More than anything, I think Chrono Cross just has a lot going in relative to the extremely limited amount of time it spends communicating anything of consequence to the player. You'll spend a lot of time focusing on Marbule and the demi-people (or whatever they're called), but major plot points are often communicated briefly before or after a boss fight at a major destination. Then the player goes hours before the main thrust of the plot is given any relevancy again.
I'm also left wondering if the game didn't receive some late game story revisions, because the scene where the dragons form the dragon god is predicated with "they're ready to get their revenge," then you see them about to do ... something. And then it ends. What?