Female characters in video games, particularly leading ones, tend towards unnatural or at the very least highly unusual physiques. I can sort of understand how this might contribute to body image issues amongst insecure women, coupled with general media (led by the fashion industry) and its quest to portray the ideal woman as a top-heavy waif. Yes, this is unfortunate. In settings where the inclusion of female characters make sense, they should be built in a manner that make sense for the role the character fills.
Let me flip this around for a moment, however.
Most men aren't built like the main characters in video games. Some might say that most gamers don't even come close to his nerdy sidekick in terms of fitness, but that's the result of poor lifestyles so let's disregard this and focus on the fact that many male leads are muscled far beyond what their role dictates. In fact, many male characters are muscled beyond what the genetic potential of most males allows for without anabolic stereoids or artificial hormone supplements. Young men have body image issues the same as women do, but it seems to give far less political capital to invest time and money into researching the mental health of males than that of women.
Eating disorders are bad, but so is body image-induced hormone and steroid abuse, an issue running rampant where I live. If you want to yell about how supermodel heroines in games cause eating disorders or alienate women, fine. But don't claim men have it any better in this regard; most guys have as small of a chance at looking like GoW's Marcus Fenix as female gamers do at looking like Lara Croft.
On the topic of the higher frequency of male protagonists...
Men have a greater potential for the development of muscle than women do. This is a matter of biological fact. There are a number of games where a female lead would seem contrived and not very believable. To use GoW again: Would it make sense to put a woman in Marcus' role? This mountain of flesh is going toe-to-toe with monstrous piles of muscle on two legs. For a female character to fill his role in a sensible manner, she'd have to be even more of a freak of nature than Marcus is.
On the topic of CoD... I don't know. I'm not terribly familiar with the setting, but my general feeling is that it makes sense to include characters of either gender when the setting allows for putting them in that role. Including female/male characters in a particular role just for the sake of political correctness, however, is stupid and an insult to the intellect of the average player.
Adventure games and other games that don't rely so much on physical combat, on the other hand, lend themselves equally well to female and male leads. Games that allow you to entirely customize your character's appearance and behavior, such as many modern RPGs, are even better at this.
Someone said earlier that the choice of protagonist gender in games like Mass Effect just lets you play a female character in a male character's shoes. I think this argument is faulty. In the particular case of Mass Effect, other characters do respond to your character's gender in different ways. If you feel you're still just playing John Sheppard with a female character in Mass Effect, you're likely either not paying attention to conversations or you have the memory of your playthrough with a male character too fresh in mind. In fact, most of the recent Bioware games seem to do reasonably well at allowing you to play a character with the gender of your choice without favoring one gender heavily over the other in terms of believability. The same can be said for RPGs such as Fallout 3, although these games are a bit less intensive on the side of non-combat NPC interaction and as such the impact of playing any particular gender becomes less apparent.