Everything they do undermines the effectiveness of Team Skull. Making it clear Aether is villainous from the very start of the game (chasing after Lillie) only lessens Team Skull's impact. The "breath of fresh air" brought by Skull's simplistic loitering is polluted by Lusamine's absurdity and obsession with the UBs/otherworldly superpowers, and even in the more subdued aspect of them "playing god" by creating Type:Null and the RKS System for Silvally. And as Phyrrhic mentioned, Lusamine's motives are incredibly shaky, and as such weakens the overall narrative of the games.
I would have much rather preferred the games focused on Team Skull. Guzma has a bone to pick with the Trial system and their Captains, while Kukui wants to keep them intact while creating the League. Focusing on that would have led to more involvement from Team Skull, which I think would have been far more effective than trying to split the focus on Skull and Aether when all that does is weaken the story. It also could have shifted the theme of the region to further emphasize "culture" and "traditions," with Team Skull trying to tear down tradition in contrast to Kukui who wants to uphold it even as Alola moves forward. And it would have still been a more "down-to-earth" narrative, potentially without bringing world-ending legendaries into the equation the way Aether did.