I'm wondering why Alyx was so important to the Vortigaunts, "If we lose her, we lose all" they say.
Plus G-Man going "Had to wait until your friends.. heh... were occupied". The Vortigaunts' motivations are almost as unclear as G-Mans lol. He also says he can't interfere with Gordon because he's agreed to restrictions. Which is why he doesn't affect you when he gets Alyx, I suppose, he can't even freeze him in time.