My point is not that there are no video games where Russia is the bad guy, my point is that assuming that because a game is made in the US it will portray Russia as bad guys shows that you are prejudice and misguided.
Prejudice in the sense that you are basing your opinion on country of origin. Misguided in the sense that Americans are more than willing to make ourselves the bad guy. In Fallout we were the aggressors and in Deus Ex our country had devolved into the exact corporate run society you guys are talking about.
I'm afraid I disagree strongly. Russians do get a really hard time of it in the western fiction, and I know a lot of Russians who find it really, really annoying. Modern Warfare is the most popular gaming (and one of the top media) franchises ever, and they constantly portray the Russians as really awful (that airport missions!!) so it's not just like it's a small example. Similarly, GTA always portrays them as the mob and Tom Clancy as generic bad guys. Combine that with them being the stock bad guys/mercenaries in most action films, and the women all portrayed as whores, and I can't really say that I blame them for being really pissed off about it. It's not even them being portrayed as 'evil', it's that they're portrayed as somehow lacking in morals compared to Westerners, or that they're easily bought.
As far as Beyond Earth, I do really worry that they'll think that morally grey area factions might be 'too much' for the average gamer and just turn it into 'the good guy, the ok guy and the bad guy'. Really hope not though.
*edited for clarity
My main point does not have anything to do with how Russia is portrayed in western culture and everything to do with the fact that you are being prejudiced yourself. You are running with the idea that "Russia will be the bad guy because that is what western culture thinks." You believe that "western culture" is misinformed or judgmental towards your culture. This leads you to be misinformed and judgmental towards MY culture. You become the thing you hate.
That being said, I want to address the other half of your arguement, regarding villians in popular culture. I can't say much about Modern Warfare has I haven't played much of it, but I believe that a US soldier does take part in that airport mission as well. I will, however, point out that Modern Warfare is part of Call of Duty which has as many games about fighting Nazis as it does about fighting people in modern times.
The fact is when you start believing that people are against you or misrepresenting you, you see signs of it everywhere. You pointed at GTA. How does GTA portray anyone in a good light? All the police and politicians are crooked liars, all the Africans are gangsters, all the Rastafarians are stoned. How often is the bad guy black? Not as often as he is albino, at least that is what an albino would say. If you think the Russians get it worse than the prostitutes or the Italians, I think you are way off.
You keep referencing Tom Clancy. Rainbow Six (the book and first game) where about a US corporation turned terrorist. Clear and present danger (book/movie) was about Columbia drug lords AND US politicians not only fighting an illegal war, but ABANDONING US troops. HawkX is about the Industrial Military complex in the US going bad. Raven Shield is about Nazi stolen art and, if memory serves, involves a South American gang. I am pretty sure the whole Jack Ryan series (Hunt for Red October, Clear and Present Danger, ties into Rainbow, and many other books) from Tom Clancy starts off with Embassy bombings in Africa by Arabic terrorists.
If we didn't pick real groups to be enemies every game would be fighting kobolds and zombies.
Finally I'd like to say that if you really believe American's won't make our selves or our history out to be villainous, I would say you are not in touch with popular culture in America. The Daily Show, Rage Against the Machine, Green Day, most James Cameron movies (Avatar, Terminator), South Park and many many others make it a point to mock or otherwise poorly portray America, Americans, or American ideals.