What if Aether isn't truly evil? Just like Colress in that they research for the sake of science, but don't quite understand the ramifications of what they're doing and then it leads to the Ultra Beasts attacking?

Meanwhile, Team Skull would just be a bunch of petty thugs who pretty much pose no threat in the grand scheme of things, but when push comes to shove, they also help you out against the Ultra Beasts. So no humans would be truly vile like Lysandre or Ghetsis, but instead, the eldritch Ultra Beasts are the true threat in the game and it's up to you to stop them with the help of the cover legendary or whatever?

I do think it would be cool if Aether was evil and delved into human and Pokemon experimentation, especially considering UB-01's resemblance to Lillie and all. But it's possible we could just be looking far too into this and it'll just be a simple invasion story.