So, with the reveal of the Aether Foundation things are looking much clearer in terms of direction of the story.

This is the second time we've heard of an organization that supposedly takes care of Pokemon, though this time they're less radical and not the enemy. They are obviously meant to be some sort of obstacle in the main game, with them having their own grunts and high rank members.

With the reveal of ultra beasts and the info we have on Aether's research, we can assume:

1) Aether really is just a friendly organization and may serve as some sort of final challenge.

Or...

2) Team Skull was just a decoy and the real evil team is Aether, doing experiments and weird shit related to Ultra Beasts. Lillie could easily fit in with this narrative, just for the resemblance between her, UB-01 and the president.