I remember playing metroid prime and swearing my robot was a man because the suit had the broad shoulder look going on. The metriod prime/girl topic brings me to think about how we judge a character by the way they dress, act, and appear on screen. It reminds me of the gender/sex debate about how women and men are both confined mainly by their physical attributes. In metriod prime, the robot suit had the sort of shape and coloring you would expect a man to wear (bulky with broader shoulders, the suit being red and mustard). I find it the case for most video games that when the gender is seemingly ambiguous we tend to, by default, assume that the player is a male.
For example, in Zelda the Ocarina of Time there is the sage Sheik. 
The suit is the same as the case for metroid prime in that the suit is broad-shouldered with muscular legs and the small portion of the face you can see has bangs you would expect from a man. You only find out towards the end of the game that Sheik is actually princess Zelda in disguise. This brings me back to the male gaze that the Lara Croft author describes: the way in which the female appearance is directed towards men by adopting the masculine standard of female appearance that emphasizes physical attributes and sexuality. This quote from Fred Davis perfectly describes what I mean by female appearance being directed towards men: “our culture’s images of women in paintings, films, television and still pornography tell us more about the male imagination than about the reality of women.” I would imagine that in the case of both metroid prime and Zelda their use of male to female physiques try to reveal the dichotomy between male and female expectations of characters in traditional games, whereas Tomb Raider’s Lara Croft reinforces Davis’ above statement.
the illusion that these characters are male are further aided by the fact that you never hear either of these characters speak in the game. Samus as far as i know never speaks and Sheik makes non gender identifying noises and you have to read what “he” says. In the context of Ocarina of Time i would argue that it makes sense for Sheik to seem male because Zelda is in hiding and what better way to hide then to pretend to be the opposite gender. Samus has less of a reason to appear male and i have still met people who think that Samus is a male. Finally i would agree that games do not portray women realistically, but they really have no incentive to do so, in part because the gaming industry is largely run and marketed to males.
As I tried to note in my previous post, Samus looks male specifically so that male gamers identify with her and are not put off by the fact that she is female. This is similar to how many female writers wanting to target a young male demographic use pseudonyms or simply their initials.