After FINALLY finishing the game, here's my take:
Everything is simple, and there is very little need to analyzation. In HL1, you were being tested by G-Man to see if you were fit to work for him. In HL2, you worked for him, the instrument some unknown side of the conflict.
Breen was right. You were not working to save humanity, you were working against it. My guess is that in HL3 you will see an even darker world full of even more insane dimensional rifts. Also, I think that in HL3 you ultimately challenge G-Man.
The story is purposefully vague because it doesn't matter. Gorden isn't supposed to have any idea of whats going on; G-Man has the ability to put him anywhere at anytime, and G-Man will only tell him what he needs to know.
HL3, much like HL2, will have nothing to do with its prequel. I can't imagine anyone saying that there is even the slightest possibility that any character from HL2 is alive, with the exception of maybe Kliner, Barney and Dog, and even then, in the next game they will be much older.
Sorry that I seem so sure of myself, but I didn't want to write "I think" infront of every sentence.
