Okay, I have thought long and hard about who the Gman is based on what we have been given in the storyline, and I have come to a conlusion that I think is not only a great explanation but also would make an awesome episode 3...
SPOILERS
The Gman is an advisor. Bear with me here; this would explain how he has the psychic abilities he has and how he is able to manipulate people. More importantly it would make for excellent gameplay. My hypothesis is that the GMan ultimately wants you to eliminate all of the other advisors so that he can sieze power with no opposition in his way. It makes since; he could have sent his cohort advisors to kill Eli so that it would piss off Alyx and You so that you could go on an advisor killing rampage in Episode 3, possibly using the Borealis to kill them all. It would then lead to an epic final encounter with the GMan advisor once you realize the truth and mabye some vortigaunts join in to help you.
Storyline wise this would make sense in many areas other than Eli's death. It would explain why he wanted you to Kill Nihilanth, since killing Xen's leader would make it easy as cake for the combine to become the new controllers of Xen's inhabitants, and it would open up a whole new area of space previously unavailable to the combine. There lies the flaw as well, since the Gman clearly was around prior to the resonance cascade, so there couldn't have been any combine. I'm sure that Valve could find a storyline workaround if they adopt this theory, though.
The ability of advisors to project themselves into human form would also lead to some questions about who is really human and who's not. It would be one hell of a twist if Alyx or Kleiner was advisor manipulated! This would be very interesting gameplay wise as the advisors might, instead of outright kill you, try to manipulate you for their own interests. It becomes then truly apparent how the Gman advisor theory would work; he just got the jump start for controlling you. Of course, all of this assumes that the advisors are power hungry and at odds with one another, but with an evil imperialistic alien race such behavior seems as if it would be commonplace.
There's my idea, feel free to let me know what you think.
SPOILERS
The Gman is an advisor. Bear with me here; this would explain how he has the psychic abilities he has and how he is able to manipulate people. More importantly it would make for excellent gameplay. My hypothesis is that the GMan ultimately wants you to eliminate all of the other advisors so that he can sieze power with no opposition in his way. It makes since; he could have sent his cohort advisors to kill Eli so that it would piss off Alyx and You so that you could go on an advisor killing rampage in Episode 3, possibly using the Borealis to kill them all. It would then lead to an epic final encounter with the GMan advisor once you realize the truth and mabye some vortigaunts join in to help you.
Storyline wise this would make sense in many areas other than Eli's death. It would explain why he wanted you to Kill Nihilanth, since killing Xen's leader would make it easy as cake for the combine to become the new controllers of Xen's inhabitants, and it would open up a whole new area of space previously unavailable to the combine. There lies the flaw as well, since the Gman clearly was around prior to the resonance cascade, so there couldn't have been any combine. I'm sure that Valve could find a storyline workaround if they adopt this theory, though.
The ability of advisors to project themselves into human form would also lead to some questions about who is really human and who's not. It would be one hell of a twist if Alyx or Kleiner was advisor manipulated! This would be very interesting gameplay wise as the advisors might, instead of outright kill you, try to manipulate you for their own interests. It becomes then truly apparent how the Gman advisor theory would work; he just got the jump start for controlling you. Of course, all of this assumes that the advisors are power hungry and at odds with one another, but with an evil imperialistic alien race such behavior seems as if it would be commonplace.
There's my idea, feel free to let me know what you think.