To be honest, I never like Chrono Trigger a huge lot (I do like it though). It took me a few times to get into it, the dystopian future kind of put me off. I eventually got around to beating it. It took a bit for me to get a hang of the story. But it was overall a fantastic game. Chrono Cross on the other hand blew me away. The atmosphere, the art, the colours, the characters, and maybe my favourite soundtrack to a game. I listen to it to this day when I want to listen to game music. I find people complaining about it are all either "The story was stupid, I didn't understand it" or "The game was too dark, not like Chrono Trigger." which is ironic considering how dark and tragic Chrono Trigger really is (The dystopian future, Schala's story was fucking sad.)
Spoiler text.So Chrono Cross's story is about dealing with Schala and the aftermath of destroying a future (he dystopian universe being destroyed caused a rift in the universe causing a parallel universe.)
The story itself was never finished. Literally stuff happens and then you go to the end boss. The game also has a ton of endings. I'm not sure how different they are, but one sounds like it's very different. I only finished it once, but the game managed to stick with me like few do. The game is absolutely beautiful. Some of, if not the best locals I've seen in a game. And again, one of the best sound tracks. I plan to replay Chrono Cross again at some point, I don't think I'd ever touch Chrono Trigger again (Maybe youtube cutscenes). Ultimately, for me, Chrono Cross is a very atmospheric game. It takes you into the world and brings you in for a ride.