I would have said some of the things you said in a softer way, but to be brutally honest, I agree with everything you said here.
I'm a woman, and despite that, I LOVE BaDIK, City of Broken Dreamers, Depraved awakening, Summer's Gone, WIAB, Dessert Stalker and Exiles. Some of these have a more solid and serious tone than others, but they all have something in common: A male protag. And that doesn't bother me at all, I still enjoy them, but Free Pass was a breath of fresh air, precisely and not only because the main character (and most the playable characters' when it wasn't Yoon) was a woman, but because it was a REALISTIC woman.
While her story seem too fantastic at times, it was completely plausible. The story was original and, like you mention, had the same mindset that a woman would have. I have played games like Luna's fall from grace, Panacea, Bad Memories, and while those also have female protags, the mindset is different: the stories are more sexually aggressive, and in some of them, you can really tell a man is behind it. Again, I'm not complaining of those games that I also liked playing, I'm just trying to make the contrast so I can explain better how well represented Yoon and the other characters were. Even if they were bold in their advances towards Yoon, you can still perceive them as believable well written women, so that's what make the introduction of a male character more puzzling. Something that used to be unique and refreshing was destroyed just to favour a small group of people who selfishly wanted another male MC, when they already have soooo many options in this website.
Also, Afterchoices said they're like Sukkhon in real life (I had no idea), so that's why I personally find the change to Sukkhon in the new version very sad. Sukkhon was already a beautiful person, who had a fanbase that loved her for who she was. Who cares if 3 fragile little people wanted her to not have a penis, if 50 people already loved her for who she was?
Again, I hope dev the best, they already gone through a lot and I don't wanna add to that, but it bums me out a little bit to see how it all ended.