Its facinating how that makes sense in your mind. So you rightfully acknowledge that the differences between men and women are significantly greater than whatever genetic differences can be observed in different ethnic groups, and yet somehow this should not influence peoples general impression of men and women?
Women are generally not associated with great physical strength because it is a much more uncommon trait, and even when women who do show an exceptional level of physical capacity show less of it than her male counterpart would. This means that what you are arguing is that games should take a trait that is a much more commonly displayed trait in one sex than the other and focus equally on this characteristic for both sexes. Again we return to the question why? Why should things be presented this way?
Also on a quick side not regarding intelligence, have you actually looked on any of the data for this? It is true as you say that there is no significant difference in intelligence based on sex. There is however a difference in intelligence distribution. If you draw a bellcurve of intelligence distribution for men and women, you get a noticable gender difference. Women are more centered around the middle of the curve, while men have more representation at both the high and low edge of the curve. So at the top levels of intellectual performance, there are actually statistically more men than women, but the same is also true for the very low end of the scale. More men than women.
Another point about intelligence is that it seems to work a bit differently for men and women. Take the top level or math prodigys for example. Men who are really gifted with math often have a much more specialized area of mental capacity. Their math genious comes at the cost of language and social skills. (So kind of the rainman stereotype.) Women with great mathematical talent on the other hand do not display this pattern. They tend to be just as linguistically and socially gifted as they are mathematically gifted.
Now what do you think that means for the top level of math as an academic field? Even if there was a 50/50 distribution bewteen male and female math geniouses (which there isn't, but for arguments sake) if the men in this category of intelligence tend to be limited to their one gift in life and struggle in other areas, how likely do you think it is that they will end up spending their life on that specific talent? Now look at an equal number of women with the same talent for math, but who also have a bunch of other options equally open to them because they are just generally gifted, would you find it suprising if not all of them chose to focus their lives on their mathematical talent?
Men and women are different, and thus are perceived differently. Im sorry if you are unable to deal with that fact, but you have yet to produce an actual argument for why the video game industry in general and this game in particular ought to display things differently than it is currently.