My personal theory is that so much was changed in the lead up to release, that they had to cut a lot of this other stuff to focus on the massive re-writes, e.g. Daisy/Guardian, Wyll's entire re-write, Karlach's and Halsin's inclusion into the game, etc. They have to pivot to these re-writes and trying to frame them in the existing story and had to let a lot of other stuff go, but that only served to make all of the late additions either feel unfinished, which they literally were, and/or create a lot of plot holes with late inclusions to the main plot that served to weaken the overall story itself. This isn't hard to believe because the
Guardian is revealed at the beginning of Act 3, the weird mandatory illithid/Orpheus false dilemma, Act 3, Gortash and Orin's inclusion feels extremely abbreviated and inconsequential, they feel like minor obstacles/mini-villains. I could be wrong but I felt Act 1 was setting us up to resolve the tadpole situation by Act 2 and that the Chosen Three were the big obstacle from there on out, hence the Ketheric arc in Act 2, but then they changed all of this at the last moment to then go back to the Netherbrain/Illithid plot last minute.
I feel like it was the result of one or two things, maybe even both.
The first is that the long rest system is still so unreliable that it's difficult to tell when it's working as-intended. Certain events, such as Raphael's visit, were decoupled from it to ensure they happen by certain points in the story. It could be that Larian realized that between Daisy, the various ways of interacting with them, the various ways your companions could respond, the way it depended on using powers, etc. was just too much reactivity to put into a system that not only didn't function correctly put a player could conceivably play through up to the goblin camp without utilizing once. So, enter The Guardian: a bland, good guy character where there's no choice: powers are fine, feel free to use them. That gives Larian a lot more structure to build around, and a lot of reactivity they need to no longer account for.
That said, if Daisy was the Absolute and/or Orpheus, then this necessitates sweeping changes to the rest of the story. This could be why a lot of interactions with the Chosen were removed, because presumably having a link to their slaved Elder Brain would impact things there. The Mountain Pass is probably the biggest example of something that was outright cut, even though the game seems to put forward that the Underdark or the Pass should be exclusive to each other. Notably, Kithrak Voss still shows up in the state you'd expect him to be in if the datamined events happened -- injured and missing his dragon. Under the time pressure, Larian elected to cut with an excavator and not a scalpel.
The other possibility I think is that Larian simply decided that there was little point in focusing on content that wasn't a typical 'good guy' playthrough. They decided late in development that they wanted to shift the tone from moody and melancholic to epic heroism, and anything they couldn't retrofit was cut. You can see this in the change of even small things that were a sub-optimal outcome (stomping the Mind Flayer), to companions (Gale's magic hunger being drastically easier to fulfill), to choices no longer having downsides (Volo's eye surgery), and massive rewrites to eliminate moral ambiguity in questlines and plot points (Halsin killing Isobel, Nightsong being less upstanding, Gale making a deal with Raphael.) However, this makes the comments by Swen that there's so many paths that some people will never see all of it a pretty poor thing to say: there is very little strong reactivity in BG3, and the alternate paths are clearly signposted. If you're thorough in your good guy playthrough, you've seen everything but the obvious bad guy stuff. And the bad guy stuff is seemingly unfinished.
Wyll's rewrite is directly linked to the change in tone. He used to be a warning against accepting deals without knowing who or what was offering them, yet finding the powers he was granted to be very useful. This would not, at all, fit with the tone and feel of the Guardian, so, he had to get changed.
