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.
I'm actually hoping that is the case...though that specific encounter was in the sewers of Athkatla, not Baldur's Gate (though I'm sure such a cabal existed in the sewers of Baldur's Gate as well).
