Why does Orpheus turn into an illithid anyway? Was it ever established that he was infected? Because he not only turns, but has the full array of abilities and retains his identity. Shifters specifically could assume whatever form they desired and used its inherent powers, but it wasn't a permanent change.

That whole debacle is really held together by snot and good wishes. During the Act 2-3 transition killing the Emperor results in an instant (and very disappointing) game over moment, and yet not an hour later Voss suggests that freeing him would be totally fine and he'll be able to keep the Elder Brain at bay just like he did in the Prism. Moreover, when Orpheus is released, the Brain is no longer under limited control by the Chosen so it's more powerful than ever, and yet we're running around without the Prism/Emperor protecting us just fine, so it invalidates that entire plot point and makes it seem like a very artificial railroading moment so that the player doesn't miss out on the Emperor's backstory and the like (I would have done just fine, thank you).

Add to that the argument about "you can only defeat the Netherbrain if you think like a mind flayer", which manifests as an arbitrary control spell channeling after which we simply proceed to beat the brain up, very elegantly and intelligently. For an entity that's supposed to be omniscient it comes across as a tantrum-throwing toddler more than anything...