They're most likely going to manipulate the player at that point in the game when they go on to defeat Team Skull once and for all, and then immediately afterwards they reveal their true intentions, they unleash the Ultra Beasts and then the player must stop them.
Also did it seem weird that when Team Skull were revealed they revealed their leader Guzma. Normally the boss is revealed during the game and not prior to its release. N wasn't revealed as Team Plasma's King prior to Black & White, Colress wasn't revealed to be in charge of Team Plasma prior to the sequels even though we knew that Ghetsis was pulling the stings. Lysandre wasn't revealed as Team Flare's boss until the games came out, but then again it was obvious. So when Guzma was revealed I thought "I bet there is someone else who is the real antagonist, because why reveal their boss now?", now I'm convinced that Lusamine is that villain even she isn't associated with Team Skull.
And another thing Team Skull don't appear to be as extreme as Teams Aqua, Magma, Galactic, Plasma, and Flare, they just seem to be a bunch of Hooligans who just want to cause trouble. The Aether Foundation definitely seem mysterious, so mysterious that they could have dark intentions involving the Ultra Beasts and possibly Solgaleo and Lunala.