Aside from all the logic that's been thrown out on this thread proving that OP is largely drawing from a skewed data set and generally making no real argument, I want to point out just how ridiculous it is that our reactions are so accommodating to OP's idea.
Think about what happens when we see this in any other demographic. More qualified white/asian/wealthy applicants apply than black/hispanic/poor. Logical response: The system is stacked against blacks/hispanics/poor people. Yet when OP says, more qualified women apply than men, and implies the logical response should be to let in more women, the response on here is to try to prove OP wrong about women being more qualified than men. The response should be to tell OP that if there's a difference, it represents a disadvantage, just like in cases above. It's been well-documented that women have considerable advantages in early school settings, and that they go to college at a considerably higher rate. I'm not going to get into that in detail b/c I'm not trying to start a flame war, but I bring it up to give weight to the idea that's it is possible men are at a disadvantage in higher ed.
Reverse the situation and we'd be throwing out terms like "misogynist" and "sexist". Instead we're accommodating this idea without pointing out the blatant hypocrisy and danger in this line of thinking. Seriously, how well do you think a thread would go over saying, "Men apply to top 20 schools at a greater rate than women, why are women getting an advantage?" This thread is a good example of how we've stopped actually thinking about the social justice side of medical school admissions, and started simply assigning protected status to particular groups and worrying about offending the wrong people. This thread should've ended in the first few replies by reminding OP that skewed qualifications in the admissions process are identifiers of inequality.
That being said, the only goal of any medical school should be to create a class that will
1) Allow students the ability to seamlessly integrate into the diverse working environment you'd find at any hospital
2) Teach to identify as equal peers with people from all walks of life.
That is the med school's only responsibility. It is not a meritocracy. Keep in mind this is coming from a white male who applied MD/PhD, where it is openly acknowledged that men are at a severe disadvantage. I'm a prime example of someone who was affected considerably by this, but I'll stand by it because objectively I can't deny the value of working alongside those who are different as equals.
I really don't understand how we can continually use this argument again and again to justify the advantages certain demographics get in the admissions process while totally failing to make that connection when the demographic in question is men.