I don't like the ending because
-It's confusingly told, even for a time travel plot. Are there two Alyxes now? Just one - if so, which one? Did they merge? What did Gordon and Eli see? In a future game will we just meet Present Alyx, who suddenly remembers that one time five years ago she went on this adventure and met G-Man and forgot about it up until the ambush in the hangar?
-As mentioned, vortigaunts and the G-Man have the ability to manipulate and/or perceive reality and time differently from humans, but being able to... retroactively/proactively change the future-past has never been a thing, and is a remarkably large jump in power that raises the question of why this has never been used before.
-The active introduction of multiple timelines or history rewriting is a deeply tricky one, and one I greatly dislike for how it not only confuses plots (see above) but removes stakes. When everything is possible, everything becomes meaningless.
-Every Half-Life has a dreary bummer ending where you win the battle but whether you won the war is uncertain; this one not only literally undoes the previous ending, it completely shifts the focus of the cliffhanger. Episode Two stood out among all the downer Half-Life endings because:
A) it set up a concrete goal (the Borealis and its never-quite-defined technology),
B) it set up a major character development (Alyx having to cope with her father's death),
C) it set up major potential conflicts (Alyx wanting to honor her father's last wish of destroying the Borealis while Mossman wanted to use it, and whether her loss would cause her to do something rash; whether the Advisor sucking Eli's brains gave them some kind of secrets of the Resistance movement that makes things much harder; whether the G-Man would replace us with Alyx a ala Epistle 3 or we'd be forced to return to his clutches in exchange for his assistance), and
D) we had so many years to stew on those exact questions, while the prospect of the Next Half-Life Game became more and more of an impassioned dream.
Now so much of that is thrown out or lessened, and the conflict is refocused on something else that, frankly, is much less interesting. Alyx's connection to the G-Man isn't, as in Episode Two and Epistle 3, something that began in Black Mesa, but is now closely tied to... an adventure five years before Episode Two that Alyx has never mentioned or seemingly forgotten about (or "our" Alyx never even experienced? See the first bullet point). Her character arc is no longer tied to becoming a leader and making decisions while dealing with grief, but being kidnapped because a past/alternate(?) version of herself five years ago made a rash, sudden, and uninformed decision based on a magical vision of the last game that was never hinted at before this game. The central conflict is now longer dealing with the Borealis while wondering what the G-Man's scheme vis-à-vis Alyx is and coping with Eli's death: it's Princess Alyx being kidnapped by the evil dark lord G-non - but don't worry, King Eli has been revived by the Triforce, and he hands you the Master Crowbar! Save my daughrer, Gordon! Oh, and that Borealis thing is still there too, maybe, I guess.
It just feels completely deflating. "Deflating" is a deliberate term on my part, because it feels exactly like this big balloon of tension was being blown up and this ending just unceremoniously lets all the air out slowly.
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