I think you are right in your analysis of the game. It's something that struck me early during my playthrough that most of the male NPCs you can have an exchange with are dumb and/or disenfranchised while women are either in a position of power or poised to get in a position of power in the wake of the player doing quests around them.
I'd like to add a couple of thoughts to your analysis.
Halcyon is devoid of toxic masculinity. Everyone is a beurocrat, so if someone gets mad at a woman simply registers a complaint. I haven't found a single character bragging about their manliness. This is good for the NPCs, less strife in their families, but it feels strange. They probably couldn't come up with the right way to portray that kind of situation and decided to avoid it altogether. The problem is to achieve this they sometimes seems to have done away with the concept of masculinity altogether. Looks like there's no way a man can be muscular and tough and bragging in this system apart from being a tossball player (tossball is so over the top it crosses the line thrice), a corporate enforcer (except they can't toughen up without filing the proper forms in four copies) or an outlaw (well McRedd is ok I suppose).
The problem with the writing as I perceive it (being a male heterosexual) is that there's no sane heterosexual male to look up to for me in Halcyon. The closest to it is Reed in Edgewater, but since that particular storyline is set up in a fail/fail way (Reed is kind-hearted but ignorant, the woman leader of the dissidents is informed on how to make nutritious meals but is a rabid extremist) it's difficult to look up to him in any way.
I think you are right in your conclusions. I found this game very refreshing with its handling of female characters, the way they were written like real human beings and all. Parvati is the best example: she's a strange person with strange sexual and sentimental leanings and she says strange things but the weirder it gets the more I like her as a person. It takes real good writing to pull that off. But yes, I think they lean too much on one side of the "man vs woman war" (in which I use the term "war" ironically). I don't think it was intentional though. I think they probably had many female writers, who of course, identifying with female characters, are naturally drawn towards them when it comes to writing a plot (as are male writers drawn to writing male heroes), and the single plots taken one by one are all good and well written, but probably in the end no one stopped to take a look at the complete picture and see that it was skewed.
Now a bit of an off topic (has nothing to do with women but has to do with stereotypes): they got it right in portraying ethnic diversity I think. In that compartment they managed to do a great work in tossing together colors and roles. First dude to die is black, but so can be your hero (and do great things). Sophia is evil, but Sanjar is good. Sanjar has an Indian accent, but he sounds like a proper Indian, not some kind of stereotype. I don't think I ever met a single far east asian character, but it probably has to do more with graphics than with writing (after all Junlei sounds very much far eastern).