They will definitely turn evil at some point, but in their own sense. I think Aether pursues a genuine, good goal, but they can't foresee the colateral damage of their actions. Just look at Team Skull, they look like little grunts, almost inmature kids compared to the real, more advanced threat. Guzma tried to become professor long time ago, he is not bad, something changed him and now he is in a rampage agaisnt the world. On the other hand, Foundation Aether has a lot of potential for the player trying to uncover its real goal. If the topic of these new games is going to be "genetic manipulation", I bet it has to do more with Aether than Team Skull, who are just "the bad guys in your way". The guy whose name I can't remember now seems to be related with Aether, but he is from Team Skull. I'm pretty sure he knows some truth.
But also, from a playability perspective, it's convenient to have two evil teams. The larger the game is, the more trainers you need. All the admins and members from an organization as big as Aether, they have a playable value that can not be ignored.