OK. My analysis:
It's been several years since HL1 and Black Mesa;
1) The female doctor says that it muct have been great to work with the two scientists when they were at the top of their field.
2) Alyx says you probably don't remember her from Black Mesa. There's a picture in Eli's lab of him, his wife, and Alyx. She's around 8-14 or so then, and Eli looks the same in that picture as he does in the one in Dr. Kliener's lab, with the whole BM research team. Since Alyx looks in her mid twenties now, we can assume it's been between 5 and 7 years.
3) The sheer size of the Citadel, and the infrastructure required to set up a presence on the scale of the Combine's suggests a signifcant timeframe between the inital conquering and the events in HL2.
3a) This suggests that the Combine/Benefactors took over shortly after the events in HL1.
My theory is that the benefactors are a collective entity that controls most of the Mulitverse. In HL1 when the portals were opened up, it showed the rest of the Multiverse a universe that wasn't known yet. The Benefactors moved in and took over and started attacking. Breen negotiated the surrender, and some of the population started to volunteer to join up with the Benefactors. They became the combine, genetic "trans-humans" that worked under Breen, that would keep working until the rest of the populace could be modified and join up with the collective Benefactors.
Note that there are two different types of gunships, in fact, all weaponry the Combine/Benefactors use. In "Route Kanal," You fight the human-looking hunter killer choppers, when later on you fight the airships that, when examined, are mechanical, but have a much more organic look to them.
Also, the lower level combine use a simple 9mm pistol, where the upper levels use the pulse rifles. Note that the secondary projectile from these is a sort of contained singularity, it quite literally takes enemies out of existance, they just float away and disappear. Not human technology.
So, we see the rift between advanced mechanical human tech and mechanical/organic tech, both being used on the same side.
The Combine are the transient forces that still use the human weaponry and devices, but the organic weapons are those beamed through the portal from the Benefactors themselves. Or, at least, manufactured or grown from machinery that came through the portal.
The G-Man is an extra-dimensional being that saw HL1 go down, and snapped Gordon up as a Mercenary, and is now renting him out to the highest bidder. Possibly to other unseen nations in other universes, who fight against the Benefactors.