I'm not surprised. Kato in general took a darker, more somber approach to the story. iirc Kato was responsible for the Zeal arc, in which the main character is killed and an entire civilization is destroyed. He was also a major influence on Chrono Cross, a game which completely lacks the upbeat character of CT.
I agree with you about Chrono Cross. I do like it, but like you said, it just lacks the upbeat character of Chrono Trigger. I'm glad the game ended the way it did and that you could revive Crono. That would've really sucked if you weren't able to. I'm sitting here thinking about it and I can't imagine Chrono Trigger without being able to revive Crono. The thought makes me feel sad.