Colress: I guess? He's somewhat treated as a villain officially, but I don't even know if I'd count him that much of a villain. Colress's motivation is realistic to me, as he's basically just a researcher that might go a bit too far in researching. But he never really does anything bad other than teaming up with team plasma, but his actions don't dictate him as antagonistic by any means. Other than maybe just allowing team plasma to do what they do, I guess. He's here because I guess some people count him as a villain(for some reason) and I need filler because most of pokemons villains are pretty shallow and I don't want to fill this list up with FE.
Ashnard: He may seem like your "evil because evil" FE bad guy, but he does have an actual Ideology that people actually believe it. And that being that people shouldn't be born into power and wealth, they should earn it. Of course he takes this to the extreme, which is what makes him a villain but still. He himself, although born royalty, wasn't going to be King, he got where he is on his own merits, which he developed this ideology in his mind. In his mind he's doing what is right and destroying the snobby, self righteous, rich class.(Who are also Villains in the Tellius series.)
Guzma: People pretty much already beat me to this, unfortunately, I just put this here because I agree, probably the best leader especially in this sense.
Lyon: What Shishoe said, you guys should stop taking my ideas.
But basically the demon king took advantage of his emotions and desperation, to add on to what he said.
Sephirian: Yeah, yeah, I know. I've been mentioning this character along with others a bit recently, but hear me out. I can't really do this character justice by just typing this, you'd have to play the game to fully understand his motivations, otherwise I'd have to explain A LOT. But basically he wants to reset the world(destroying the current one and creating a new one) because it's filled with so much terrible things. Including so much violence and bigotry. Well, that's the basic summary of it anyway, But to me that's just something I can relate to. Because some days I just feel like this world is full of so much pointless conflict and hatred that could all be easily avoided, but isn't due to how people think and judge each other. The "we could've done a lot better than this" sort of feeling. This itself I can go into a lot more depth, but I don't want to make this too long.