The main villain aspect will be one to watch out for. I have a feeling that problems with Baldur's Gate go beyond Mind Flayers.
The D&D 5e campaign that acts as a prequel to BG3 showcases the Cult of the Dead Three as well as denizens of the Blood War in Avernus (demons/devils). There is a lot Larian can pull from. A friend of mine is hoping for a trip to Avernus and meeting Jon Irenicus again...but I think that would be a bit much lol.
I'm really hoping the Mind Flayers tie into their BG2 counterparts. In BG2, there were Mind Flayers hiding in the sewers beneath the Temple District. There you find a letter outlining their connection to a group called "The Hidden" and their desire to infiltrate/increase their forces. This seems like a good jumping point for BG3 and provides ample opportunity for there to be a "Big Bad" behind the scenes.