My main issue is that it's barely (if at all) integrated with the characters' individual plotlines. The tadpole and the companions' personal quests exist in isolation from one another. You could remove either and the other part will not be affected, safe for perhaps Lae'zel's storyline (to an extent).
Up till prologue, all companions are from different part of The Forgotten Realm. They don't know each other. They aren't friends with other.
Then they all got on the nautiloid for whatever reason and got the todpoles. That is an isolated event in their lives.
So isn't it logical most of that their personal quests has nothing to do with the todpole?
That also give as much freedom to player as possible, from choices to skipping.
To end the game, all you need is Sarevok, Gortash, Orin, Ketheric and netherbrain. All else can be consider side quest. (Or maybe Gale blowup.)
Orpheus' role in the plot is handled very clumsily as well. If he's the one holding back the influence and the characters are perfectly fine with the Netherbrain being unshackled and him being out of the Prism, then what's stopping us from killing the Emperor early and simply remaining within the Prism's power's range? The Act 2-3 interlude makes the character transform instantly as soon as the Emperor dies, while "betraying" him at the end of Act 3 allows to go ahead and use the Hammer first. Orpheus' honour guard must have had some plans as to how to liberate him, for them to invade the Prism without the Orphic Hammer - it being yet another plot device which exists solely as an added complication. And if Orpheus blocks out the illithid influence, why would we have powers and telepathy in the first place?
^^^ This is very good catch!!! For free Orpheus path, the (non)requirement of Orphic Hammer is definitely a plot hole. ^^^
PS: Second thought, in interlude the Emperor is killed, but before final battle Emperor run away. Does that make a difference? Or does that become another plot hole, hahaha!!
As for the "strong mind", it's not the resistance to illithid influence, but retaining the memories and the personality upon transformation is what's an issue. An illithid kills its host upon completing ceremorphosis. Orpheus simply changing into one with no explanation given (one would assume he actually becomes a mind flayer rather than simply assumes a form of one if it's irreversible and it specifcally requires an actual mind flayer to counter the brain, for whatever reason (it amounts to focusing on a spell, which you'd imagine a powerful enough spellcaster with an intelligence/wisdom to match would have been able to do regardless)) is another moment that is hardly making much sense.
Orpheus used a todpole. In D&D soul/mind can be separate from body. So it is possible to have body go through physical change but keeping the soul/mind intact. It is a magical world

But nonetheless, that physical change does affect his mental status. That's why he sought death after the final battle.