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X/Y and DPPt have a lot in common, but I don't think people discuss where they differ enough. Team Galactic may be silly, but they're still pleasing enough to look at, and all of their top brass look cool, or failing that, respectable: as far as anime characters go, none of them are totally repellent. Team Flare looks dumb, their leader looks outrageous, and their admins are redundant. There are five of them, and they're all basically interchangeable grunts from what I recall. If I'm wrong, please tell me. Malva and Xerosic are the only ones who look cool, and in Xerosic's case, it's only because he's scary looking, which is good for a villain in his position. But Xerosic goes from nasty to just plain weird in the post-game. He's kind of inconsistent. I guess he likes science, but he seems genuinely enthralled by Lysandre's genocidal machinations.
Speaking of those, Lysandre seems way crazier and more malicious than Cyrus. What he intends is nothing but murder for the sake of aesthetics. The way he and everybody else who’s in on it talk about his plan just makes him seem like a complete lunatic. One could argue that Cyrus is also chasing after a certain aesthetic, sure, fine, whatever, but the poise with which he presents his true aspirations makes him seem more level-headed and less like a raving lunatic. Like this is something he actually thought through, whereas with Lysandre it’s just, for lack of a better term, melodramatic schizobabble capsizing into a pity party. In short, Cyrus is more dignified. There’s also the way the Gen 4 characters note that Cyrus himself cannot escape the “spirit” he detests so thoroughly. Gen 4 raises a lot of questions about the human condition that Gen 6 does not – at least, as far as I recall.
Lastly, Cyrus doesn't speak of sparing the chosen ones or anything like that. He's thinking on a higher level than Lysandre, who at best seems to be thinking of creating an ideal country, as opposed to an ideal world.