Do you think that Bardugo always planned to have Alina lose her powers? If she did, that’s confusing because how can she say that her powers were a metaphor for body autonomy and desire, do the whole shadow and light thing with the Darkling then leave her powerless and a nobody/Mal’s wife?
That's a good question. It certainly doesn't look like it was planned from the beginning (let's be honest, there is no aspect in those books that looks like it was well-thought-out or planned)
The ending does look disjointed and thematically inconsistent with the rest of the books. In books 1 and 2, Alina is shown miserable every time she is with Mal. She's repressed, weak, miserable, self-loathing and ashamed of herself. She is genuinely happy to finally "unlock" her power. The only natural, satisfying development from it is Alina accepting her identity as Grisha and cutting off everything that hindered her (cough, Mal, cough). Yet, somehow she does the exact opposite, and we are told it's a good thing. Maybe Bardugo wanted to subvert a coming-of-age trope, but it was a total failure. You can see that even those who claim to like the ending are hella confused because they can't agree on whether Alina didn't want her power at all and gave it up willingly or it was taken away because she was corrupted by power-hunger. The former isn't supported by text, and the latter (s in Alina's supposed corruption) doesn't get a compelling development. Not to mention the fact that if her powers were a metaphor for body autonomy and sexual liberation, taking them away as punishment invites deeply uncomfortable implications. Your body is yours as long as you play by rules? Horrid. The ending was such a mess people's minds refuse to accept it and come up with romanticized confabulations.
Then there is the whole "Mal being the third amplifier" thing. It's completely illogical, because Mal doesn't show any properties of an amplifier. Meanwhile, Aleksander is established to be an amplifier from the very beginning, and it remains completely irrelevant to the plot. It's obvious that a much more elegant solution would be to make Aleksander the third amplifier and to get Alina to kill him. This way, his death would be more meaningful and logical, and if Bardugo had reservations about making Darklina canon, this problem would also be solved. A tragic, bittersweet ending practically writes itself, yet the author vehemently rejects it for the sake of making her favorite sexist blade boy relevant.
I've seen different arguments pointing to the fact the ending was changed: Bardugo's weird change of heart about Darklina, Alina forcing Aleksander to use merzost (an act matching the collar in its invasiveness), Alina telling Mal that she didn't really belong with him and that she would never give up on her power, Alina's odd donkey dream, or Nikolai's initially planned death, so the most logical conclusion is that the change was abrupt and ill-conceived. I've read other Bardugo's books, and it seems like hollow, unsatisfying, incoherent endings are a recurring pattern. In simple words, she has ideas but has no clue how to develop and conclude her plot.