The choice to turn the tadpole that kicked off the entire story and ties the player into the greater themes of the game into a red herring only to have its narrative role supplanted by a a MacGuffin in the form of the astral prism that has no connection to the player character sure was baffling to me.
The central premise of the story was established with the very first reveal trailer and it's that you are going to turn into a mindflayer with all its soul-destroying body horror implications. That is what makes the story interesting and unique and it's what the plot should focus on. The game tries to do this in Act 1 because your ceremorphosis still functions as a golden thread that ties most of the side content back into the main story about you and your special tadpole.
My expactation playing the EA was that the main story would take more of a center stage as you progress into Act 2 and try to find out more about the nature of your tadpole, your role in these events and what you can do to avert the threat to both yourself and the sword coast.
What happens instead is that you get a dream visit telling you that everything you did in Act 1 was basically a waste of your time and you should put more tadpoles into your eyesocket instead of worrying about the story you've played up until that point. The looming threat of ceremorphosis, the moral dilemma of using the tadpole, the pursuit of removing your parasite - none of that really matters anymore even though it was supposed to be your main force driving your actions.
Suddenly, the game is no longer about this very personal struggle about saving your soul but more of a generic heroic fantasy "save the world" type scenario with all the baggage that comes with it. The problems with this narrative shift don't immediately manifest themselves in Act 2 however since the story of that act functions more as a sort of self-contained intermezzo that is interesting enough in its own right (with Ketheric Thorm being probably the closest thing the game has to a charismatic antagonist).
I think enough was said about Act 3 already but suffice to say, this is where the chickens really come home to roost. With the player character being bereft of their personal motivation, all of the side content you do in Act 3 (although being of similar quality) ends up feeling aimless and without purpose. Whereas Act 1 tried to tie the side missions into the main story, Act 3 does the exact opposite. Not only is there no golden thread connecting all these loose story ends with the main story, they actively weaken the main plot just by existing due to their bad integration. Act 3 creates a perplexing situation in which the urgency of the main plot actively hampers your ability to take the side content seriously while the act of playing through the side content undermines the severity of the main plot.
That being said, I don't know how you would even begin to "fix" it. They basically killed what made the story interesting at the end of Act 1 when the game decided it was no longer about turning into a mindflayer (until the last hour of the game where it suddenly remembers its premise). Shit is cooked.
