The system for qualifying is pretty good but not perfect. Yes, it is heavily favored toward women. They could lower the women's standard by five minutes (or raise the men's by five minutes) and it would make a lot more sense.
Also, now their standard of the "real" qualifications (what it actually takes to participate in any given year) is very inclusive, but doesn't reward the FASTER runners. For example, one year you had to run like 1:24 lower than your age-group standard in order to actually qualify. So that means a 34-year-old man would have had to run a 3:03:36, but a 40-year-old man would have to run 3:13:36. I believe the preference should be to the faster athletes for that year. Weight it a little bit so the faster people get in. Remember, if you don't get in, you get automatic entry the next year, so you're not really "denying" anybody a chance. It's just deferred for one year.