i would like to focus again on the reason(s) why this setup "someone must become a mind flayer" feels so bad. I think I have found the main culprit: the fact that these scenarios, as they are, turn the theme of your personal story, which you set by how you deal with the tadpoles, into its opposite.
. . .
What does everyone think? Am I onto something here?
Well said. Yes, you are correct and I hope that Larian is reading this thread. I didn't play ME3 so I can't comment on that comparison but the ending feels like a defeat for the Tav who avoided "absorbing" tadpole and using the illithid powers. And it doesn't feel tragic - it's more bathos than pathos.
"well it seems that the uber-brain was really a nether-uber-brain and that means all your attempt to avoid become a mind flayer have failed. Also, dilithium crystals"
The ending needs to be revised and I hope that happens sooner rather than later.