Personally I disagree with the idea that Kojima has anything 'wrong' between him and weapon. Simply because he includes women as enemies in some games, or 70% naked through out most of the game, or heaven forbid have some kind of social comment on what has happened to civilians through out the world because of wars does not, in my view, mean he has any issues with women...
I cannot speak for the zoom-in feature nor the dating sequence for I haven't played Peace Walker. However, I found it impressive that he would even have female bosses between metal gear 1-3. True while Sniper Wolf's main point could be seen as to die, or make us worry about the girl following us around, her death was also use to feel for Otacon, to for just a second, give the sense that he had balls and though about more than Just anime and giant robots.
As for Fortune... Well... in general 2 was a bit odd so I didn't give the bosses in 2 any thought as in to what they were actually there for aside from being a kind of terrorist group... Though I really don't see a problem with Snake/Raiden finding and using 'girly mags' to distract guards.
3... The whole thing is a lamp shading of most of those 'I'm a guy that women just seem to take their clothes off around me for no good reason' style spy movie, of course Eve's gonna have her jump suit zipped down to basically her crotch. As for The Joy and her baby issues, while I know I cannot fully explain what is trying to be said about sending a woman who was heavily pregnant, I do know that the scar she had from having the baby taken away was just suppose to be symbolic, since it's a snake... And you're snake... and the game's Snake Eater... and so on.
Finally what little I have played of 4, I really thought they was just trying to grip at her emotional heart strings in that, while we are fighting animal women gone insane, is the fact that they are insane because, big shocker, bad things happen to good people when wars break out. I'm sure that, while not becoming exactly this insane and well armed, how mentally, physically, and emotionally tortured these women were, and how crazy they turned are not that far off from how some real women ended up.
... course those are just my views I could be completely wrong and both I and Kojima have terrible, terrible issues with women who knows.