I was actually thinking about this very point earlier.
Interesting that, Chrono Trigger portrays humanity as being basically good; the enemy being Lavos, something foreign to humanity and our planet for that matter, and Crono and company, representative of humanity, ridding the world of this threat, thus saving humanity.
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However, in Chrono Cross, humans are portrayed as having a darkside. This is mostly evidenced by the chain of events surrounding the Masamune.
Humans also subjected demi-humans or otherwise drove them from the demi-humans' homelands.
Also, Crono and company have some dissonance, doubt and regret regarding what they did, traveling through time, changing history, and defeating Lavos. Indeed, perhaps in what they did, some people were adversely affected.
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Why they decided to change the mood up for Chrono Cross, I don't know. I've just always seen 'Cross as a much more thematically mature plot than 'Trigger.
That's not to comment on the complexity of the plot, but 'Trigger doesn't really touch on themes like environmentalism, existential, racial, or any ethical issues at all. At least, not directly.
Sure, in the ending of 'Trigger, Marle and Lucca mention fate, but until 'Cross, we only perceive that mention lightly.
