If you talk about Hollywood movies, then yes, they've been bad.
But the main story of BG2 was also riddiculous.
So we have this epic level elven wizard who tries to turn himself into a deity and almost managed to destroy the tree of life in the process. What does the elven queen do ? Not give him the death penalty. Not put him in prison for life. But sever his connection to the tree of life, thus making him unable to feel feelings, and setting him free on the world, to "teach him a lesson" or whatever. With super predictable consequences, the wizard tries to make himself into a deity AGAIN, of course again through the very same process as before. Well ... duh ? What else was supposed to happen ? Who in their right mind could not see this was going to happen ? They literally removed his ability to differ between right and wrong, made him into a pure example of a psychopath.
Also, Larian wasnt given a choice about the main plot really. It had to have Mindflayers, WotC said.
To what has already been said in the thread, Mindflayers need one adult brain of a sentient race every week to maintain themselves. They cant eat anything else as substitute.
So - benevolent Mindflayers ? Independent Mindflayers ? Mindflayer slaves ? Mindflayer mass production ? Those are all absurd proposals.
Every Mindflayer is an enormous demand on resources. To run just a small colony of 20 Mindflayers, you need multiple 10,000 of slaves, so you can farm them for 1,000 adult brains every year. Alternatively you need just as many free people that you have to hunt down.