Every time people lament changes to the lore that amount to "not every member of species X is irredeemably evil" and claim the game is removing villains from it, I think how villains of so-caleld evil species fall into two cathegories: a) bland and boring and b)have something else, unrelated to their species going on for them, that makes them interesting.
I would say that many Mind Flayer villains are quite interesting because they are Mind Flayers.
Personally don't really find the snack sized Cthulhu aspect that interesting. What really interests me about them is the lore about them once being a great empire of douchebags who were overthrown by those they oppressed (gith) who then took their place politically and now hunt them down. Says a lot BG3 focused on this lore over the Cthulhu monster aspect. Just some good lore building which could have (and I'm sure has) gone to any other races.
How would an oppressed people even have a chance of overthrowing rulers who could read and control their minds?
Gith became resistant to the mind control over the millenia. This is why in 5e the race has psychic resistance. The duergar were also slaves of the mind flayers and this is why they have psionic fortitude. There's some other races that have been altered due to being enslaved (derro, kuo-toa, quaggoth), usually resulting in some form of psionics and madness.
Part of what makes mind flayers interesting because their society touched and left scars on a lot of other races. Gith are just the loudest about it in part because they live in the Astral Sea where time doesn't age them so, outside of dying during raids, many of the gith who rebelled can easily still be around leading to the rebellion being fresh in the gith's minds (as opposed to the duergar for example who live on the material plane in normal time and have had empires rise and fall and numerous generations since the enslavement).
Seems like a pain, but possible. It would make a good story.