Does anyone get the feeling that the Vortigons are maybe named as an homage to the Vorticons? I mean, surely someone at Valve got their start with id Software’s “Commander Keen,” right?
[nitpick]According to HL2’s subtitles, I believe it’s actually spelled “Vortigaunts.”[/nitpick]
I thought the same thing. In fact, according to the Keencyclopedia, Commander Keen’s Vorticons are “controlled by the grand intellect,” which is an awfully close parallel to the Combine/Nihilanth/Vortigaunt relationship in Half-Life, as well.
I finished the game tonight. Awesome. On a scale of 1 to 10, I give it a 9.9
(It loses 0.1 points for having the most annoying installation process in the history of computing.)
As for the last couple of chapters and the ending:
[spoiler]I like how they took away your weapons without resorting to the cliche “character gets captured and then escapes” routine. And I REALLY like how the super gravity gun was created by accident. I guess that trying to disintegrate a zero-point energy source is not such a good idea 
And that super gravity gun is freakin’ sweet! You didn’t need another weapon after that thing was created.
BTW, did anyone else notice that the alien grenade (from the pulse rifles) seems to be based on the energy orbs that you find in the shield generators and plasma beams? Little things like that go a long way in providing atmosphere. I can imagine how some poor repair guy working on a shield generator got disintegrated by accident, and then his superiors looked at each other and said “Hmmmmm, we should look into making a weapon based on those orb things.”
As for the ending, I wholly expected to end up getting transported to Xen (or some other dimension) along with Breen. That the machine just blew up and killed him caught me by surprise.
I don’t think that there’s any ambiguity about whether Alyx survived. Sadly, it looks like she doesn’t. Heck, it’s only because the G-man intervenes that you survive. I don’t expect that Alyx’s father or that turncoat chick (I don’t remember either of their names at the moment) make it, either. At least the citizens of City 17 will remember you as a great hero who sacrificed your life to save them.
I never seriously considered the possibility that Breen might be right, and that Gordon might be dooming humanity. It looked to me like Breen had created some kind of “master race” (remember his speech to the Nova Prospekt guards) and was trying to supplant the normal people. Remember, he was using some kind of “Supression Field” that kept people from reproducing. He was probably going to leave it on until the civilians all died out.
No, it’s Breen who was the genocidal maniac.[/spoiler]