While the story has plenty of problems - mainly the pacing and the lack of consistency going from plotline to plotline, aswell as lack of motivation that leaves plenty of characters just...existing - i think it handles most of its themes well, if a bit on the nose.
Let's get the bad stuff out of the way first: The ending is pretty rushed, and has some awkward messages(which i do not believe represent the author's personal views, but the character Minako in question). Some plot points could've been given 2/3 more chapters to develop, which leaves a pretty unsatisfying taste in my mouth.
The controversial(but good): This story is built on a pretty simple and basic concept, and that is: women should have control over their own bodies. This isnt a simple commentary on rape, its a commentary on objectification as a whole. At the end of the day, the manga is not saying anything aside from that. Where this can be lost in interpretation is the lens through which we see this message being told.
The characters are for the most part frustrated women. They're used to showcase the problems the author probably faced or saw some face in their lives, building this nihilistic and fatalistic view where, deep down, everyone is defined by their gender roles. Even those that try to escape it, are not able to. This doesnt go just for the men, who are in multiple scenarios rapists or wannabe-rapists. No, this goes for the women too, who repeat the mysoginy and treat eachother like trash behind eachothers back. Even the ones such as Ayaka that try to be truly independant, arent able to and still rely on a man.
Wadajima, a man who manages to fullfil his gender role easily and with a lot of success on society, also can't escape his need to impress Misato, a women.
And where one could complain this is misandrist or too ''feminist''(whatever that means these days), the manga goes out of its way to also - via Niizuma - showcase the struggles of being a man. While the professor Misuzu at first condemns and even blames Niizuma for being raped, saying a man cant possibly be a victim, at the end of the day, that was simply projection on her part.
Even her ''preaching'', saying ''its the men's fault that women suffer, who else could be at fault?'' is stated after an entire page showcasing WOMEN being terrible to other women.
The manga isnt as self indulgent as it seems(but it can be at times, definitely). It uses the traumas and fatalism of its characters to showcase how society is trash, and also how that unfairness of society made the characters in question lose the capacity to see hope and be unbiased when dealing with people. Which is why the conclusion at the end consisted of the main characters forgiving eachother and believing in hope again.
