The whole voice-in-your-head plotline would probably have worked better if Tav wasn't aware from the jump that a Mind-Flayer had tadpoled him.

The Emperor interactions would have worked better if he treated Tav as more of a hostile entity, instead he keeps trying to play up the 'I'm your friend and protector' angle, but he knows that we know we've been infected, so dispense with the ploy, it's not metagaming for Tav to have no reason to trust the mysterious voice in your head telling you to slurp down every tadpole you find, and the Emperor should have tried to work around that instead of crossing his fingers and hoping we're the worlds most empathetic victims

As it is, Tav is conditioned to distrust everything, while the voice does everything to justitfy that. Except that the game really seems to think we the players aren't motivated to do the same.

I think the Emperor plotline, and maybe the main plot of the game, jumped the tracks for me when you're forced to kill the Githyanki honor guard. When the game shows it's hand like that by forcing us to side with the Mind-Flayer I started to be worried it had worked itself into a corner.