I think most games, especially role-playing games, fall short in the final act. Despite that BG3 is still well worth the price of admission, though I'll think twice before joining another early access.
I hope Larian consider keeping up with the game now that it's launched, but I've gotten the impression from interviews with Swen that he's a bit 'over' it. The amount of work it would take to rejigger the main plot in BG, might just not be worth it for the number of people who think the problems with the narrative are serious enough to even warrant it.
Yeah it's been my worry, too. Ever since Swen said he's pretty much moving on to a new 'secret' project and that he's pretty much done with BG3 (of course that doesn't mean his team isn't done with it, but yeah, there is that).
On the topic and I know it's been said a lot, but I really hate the way the game took away all the consequences of using tadpoles. I remember in EA I loved testing both scenarios - a purist "Daisy is evil, we shouldn't trust them approach" and "Give me all the power" and how very different those 2 were from the get go.
Aside from getting a bunch of dreams (which you wouldn't get if you didn't use the powers at all) and those special illithid powers (which were different depending on class) what was so cool were the reactions of your companions to the dreams, new powers and getting closer and closer to becoming mind flayers. All those moral discussions you could have had with them are completely gone and therefore a lot of character building is lost. And yes, some of those conversations would pop up even on a 'no tadpole' run but it would take way longer to get there. And what's funny is the game still kept some of those conversations in the final release, companions still say they got new powers (yeah, no I checked buddies, the cake is a lie) but the overall morality discussions are gone.
Of course that meant in EA, if you truly were a purist, you would never ever get a single tadpole related dream, so I kind of understand why Larian forced that on us (on release my 1st run I was a purist until I realized that using tadpoles had no consequences whatsoever that was after my 2nd dream btw. - then I put a tadpole in my tadpole so I'd tadpole even harder). What Larian should've done is - have purists get dreams, different dreams than those who embrace the tadpole and obviously at a much slower frequency, and maybe have them closer to what we got in the final release of the game while whole unhinged tadpolers could have their dreams be closer to what we had in EA.
I also understand why they decided to take Emperor from whatever plot he was a part of in game (I doubt that they created his character out of nowhere, my suspicion is that he was one of the 'potential' allies further along the line - also, he is in the opening cinematic I believe, the mind flayer tadpoling Tav has a very striking resemblance to Emperor) and repurposed him into the guardian, at the expense of whatever interactions we would've had with Orpheus. I don't like it, but I understand why that decision was made. Daisy was suspicious as hell from the get go, while Emperor seems a lot more... benevolent? Unless you take your time to annoy and distrust him over and over again and this is also where plot holes around Emperor start to pop up. Especially when he shows you that he was basically responsible for Stelmane's comatose state... I mean: actions have consequences right? So why I can't discuss this major discovery with anyone? It's not like he told us to stay silent, just stay obedient and be a good little puppet.
Because of that massive rewrite to fit Emperor and twist the current plot around him I doubt that Larian would be brave enough to remove him and return Daisy and I am fine with that. But for the love of all that is holy, rewrite the scenes he's in to make them make more sense. Especially in act 3 every single time Emperor pops up a major plot hole is introduced.