Wait, why do we have to have the option of choice for everyone? Shouldn't we make games where it makes sense for gender, race, country of origin to fit into the plot? I mean, one thing about Cmdr. Shepard is that he/she's just a empty name. We shoehorn his/her lack of backstory in with a couple of options. But we don't get anything more than that. It's not like we can go: "Hey! He's from..." (Googling) "...Mindoir. How come he's white? The Mindoirians were uniformly of African descent" because like Shepard, "Mindoir" is just a name.
Conversely, in Overlord, which is a satire, it makes sense to have a male protagonist, because he's basically a stand-in for Sauron, who is referred throughout Lord of the Rings as being male.
I think you're attempting to make a molehill into a mountain here by going the "let's please everyone" concept. That's not how compromises work, nor is it how problems get solved. You can't please everyone, as anyone who's ever worked towards attempting to mediate a dispute quickly discovers. But you can make sure that no one gets unfairly shafted. I mean, where it makes sense for a character to be a white American guy, do so. But maybe you have a theme like "dealing with discrimination" so you make him black. But maybe you also want him to have a British accent, because, well, I can't think of theme or trope for that, but what the heck, he's British, so the character becomes West Indian. Oh, and it's discrimination in general, so you make the him a her. It makes sense, within the context.
Likewise, the prevalence of white guys from America make sense, because it seems like the vast majority of games center around "Soldier/pseudo-soldier solves [insert problem] by [insert explosion+guns]." Most of the developed world (read: Western world) is populated by majority white populations, who are the primary recruits for armies, and no one spends more money on their army than America.
I think that once we escape from the "action is the only thing videogames do well" mentality, then we'll start to see some changes. It's interesting to note that videogames have arrived as new media in a time when we're especially socially conscious, and thus can call attention to its short comings in that department. It may help to hyper-develop the medium (or, possibly, stunt it's growth).