For one you don't need to be in a VR world to deceive someone. Even if somehow the nature of the patriots and their motives was a lie (which I can't fathom why that would be at that point, in storytelling a truth at the end is very beneficial to show how everything before that was a deception before the realization), that is still not an indication that it's necessarily a VR world.
Let me reiterate, I'm playing Devil's Advocate here.
I know it doesn't
have to be VR to be a deception, but as whacky MGS theorycrafting goes (and that is all The VR Theory is), this one ties in quite nicely with the game's themes, specifically the nature of reality in The Information Age, disinformation, and the relationship between the player and the game (Raiden spends most of the Arsenal Gear section questioning the reality of the situation, and since Raiden is arguably the player...)
Yes, a truth can of course be beneficial in story telling terms, but when the game centres around Disinformation, both thematically and narratively, and wants the player to consider these beyond the game, it can be equally beneficial to leave it ambiguous. Think of all the films that end on ambiguous notes: Total Recall, Inception, anything by David Lynch etc.
In fact, one of Kojima's major influences when writing MGS2 was The New York Trilogy by Paul Auster, three stories that offer no easy or conclusive answers to it's mysteries, and that asks it's readers to consider it's philosophical and metanarrative questions. So arguably, leaving it on an ambiguous note would be more beneficial to the point Kojima's making.
Speaking narratively though, (and this isn't a particularly important point, just a thought) why would the AI reveal their masterstroke to a pawn that they clearly hold in such contempt? Is it so they can gloat about how great they are (which is a very human thing to do for something that holds humanity in such obvious contempt) or is it part of their deception and manipulation of Raiden to get him all fired up and fatalistic for the final confrontation...?
You don't actually explain why this makes them suspect in this situation though. It's basically saying that their design originated from the white house and evolved from there.
That's one interpretation, sure, but you're arguably stretching what was said to fit your point because, let's be honest, that's not what the Colonel said at all.
"Hundreds of years"? "A consciousness formed layer by layer"? "We are the very discipline and morality that Americans invoke so often"? Nothing about design or AI.
The opening of the Colonel's revelation shows that they are, or at least think they are, something more than simple AI; a consciousness born hundreds of years ago from America's centre of power. Forgetting that MGS4 completely blows that out of the water, MGS2 itself had three points I can think of off the top of my head that show that they are purely AI which contradicts that opening gambit.
Firstly:
Raiden: How is that possible? The AI was destroyed?
Colonel: Only GW...
We can't necessarily believe everything the Colonel says, but this directly contradicts the "revelation" by implying that they are different AI to GW (as you mentioned later in your post) rather than a two hundred year old consciousness. Which is the truth and which is the lie here?
Secondly, The Colonel is affected by the virus. Only the AI could be affected by it, so this again calls into question the veracity of the Colonel's opening revelation.
Thirdly, they didn't have AI "hundreds of years ago" and they don't do AI design in The White House.
Taking all that into account, that's why I think it's
possible to argue that The Colonel could've been lying even during the final "revelation".