Upon further thought, the whole mindflayer ship opening is quite possibly one of the worst ways to start a story. The entire plot is suddenly pigeonholed into an urgent quest to find a way to get rid of the mindflayers, which turns out to be false both narratively AND from a gameplay sense. It really messes with player expectations a lot.
I also think the mindflayer tadpole plot device is quite boring at this point. Seems to me like literally every other subplot in the game is a lot more interesting with more potential varied outcomes than the zero sum 'what the hell are these tadpoles and how do they factor into the big bad's plot' thing. I really think we should have gotten an opening phase showing us hints at all the other subplots before the mindflayer stuff happens and screws everything over sideways.
I only wonder if BG3 is putting too many eggs into everything being dark and mysterious, because we literally don't find any meaningful answers to anything in regards to the larger plot at our current point in the EA. I've said this before, stuff like this is why expectations in regards to the writing for people who are really into crackpot theorycrafting are sky high (like all the insane people guessing that Gale might be a reincarnation of someone who fought against Mystra or something). But to everyone else who prefers a more well rounded experience, it's not surprising that things feel a bit shallow.
And the higher you go, the steeper you crash if you fall. The writers of the Mass Effect series know that all too well.