Here is a plausible explanation I have developed that could explain G-man's nature.
Now, my theory, rather then having to do with some bs like "GMAN LOOK SIMILAR TO FREEMAN* and things like that, it rather has to do with the language he uses in his speeches to freeman.
Now what kind of talk does G-man consistently use when addressing Freeman? That is easy, he uses what appears to be business lingo. He constantly uses words like "Job, services, employers, investment, appraisal, offers, contracts, ect."
What are all the other references to him by other characters about?Well lets see, the supposed ambiguous reference to G-Man made by Breen is that "Freeman's contract was sold to the highest bidder."Because of this, we could infer that it is highly likely that G-man acts as some sort of extraterrestrial Businessman, a contractor of military service.
He is neutral to the actual conflict, all he seeking from it is a profit. This explains why no one who sees him, seems to hold him as either a complete ally or an enemy. Eli anxiously talks about his "mutual friend", in a way that suggests he isn't completely a friend. The vortigaunts seem to dislike G-man and his influence and possibly complete control of Freeman.
Its even possible that in the first game he was working for the Combine and helped set up conditions for them to take over The borderworld, Xen. He might of even worked with Breen to make this happen. His sides could easily change, and he is constantly talking about how he is getting new offers for freeman's service, so he pushes Freeman around and misguides him.
I could even dig up more evidence and noticed some other things before...but that generally explains it. Still, he is a big plot tool, something to keep you wondering, I could be wrong.
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Sorry if the grammar sucks in this post. I was lazy so I just copy pasted my chat pm to a friend about my G-man theory.
http://www.youtube.com/watch?v=0arkuLskbDU