I take no offense at anything you say Final, in fact I welcome the discussion. I'm not so personally invested in the show that my feelings get hurt if someone criticizes it.
You level some criticism at the game, or at least lump the anime in with the game and criticize them both as if they were the same entity. If your criticism was aimed solely at the game then we would be in almost total agreement. I have not played the game and have no intention to; from what I've heard of it, it is just a straight up harem H-game and all your criticisms would be applicable to it.
The anime on the other hand is a textbook example of genre deconstruction, in which the tropes of a given genre (in this case the High School Harem genre) are adopted as the premise of the show and then events are allowed to play out to their full conclusion (in a more realistic way than is typical of the genre being deconstructed). It shows the negative consequences of the tropes being used in order to criticize them. It's like accepting a premise of an opponent's argument in order to construct a Reductio ad absurdum.
The show uses the 'protagonist has sex with every female in sight' cliché (among others) to show how absurd the cliché is and how if it happened in the real world things wouldn't turn out all lovey-dovey like they do in the majority of shows. I thought before that you hadn't recognized the show as a deconstruction, and that you thought it was just playing the tropes straight like every other harem show. If this was the case then it would be a valid criticism against the writers' communication skills.
However, in your last post you acknowledge it as a deconstruction yourself, but then you go on to condemn it for using the aforementioned tropes as if it was approving of them rather than criticizing them. You blame it for being misogynistic because it satirizes the very tropes that you yourself dislike. It's like reading Huckleberry Finn and then accusing Mark Twain of being racist (to use a topical example). I don't know how anyone can watch the series in its entirety and still think that the writers are advocating misogyny. They seem to have similar grievances with the harem genre as you have (and I have for that matter). As far as I can tell your main gripe with the show is that the writers agree with you.

Concerning the violence: I went back and watched the end of the last episode before typing this and realized that
no violence is shown on-screen. Every time there is a knife stab or slash the camera cuts away or else goes to a flashback of something else. All you see is some blood flying from off-screen and then the aftermath. It's done in a similar way to the shower scene in
Psycho, but even that was more graphic. They could have easily turned it up to 11 with the violence and made it far more graphic than it was but they didn't. The only reason it seems so violent is that it's contrasted with the rest of the show (you even mention this yourself). But even if it had been as violent as you say, I don't see why this is a bad thing exactly. The whole show had been leading up to that point, it's not like they just put those scenes in as an afterthought for shits and giggles.
The criticism of it having too much sex (or however I phrased it); with a cast so large you simply don't care by the end of it how much is going on; it turns it into a game mechanic rather then something important, making the effect of someone going crazy because of it much more muted - why should there be only two crazy people? why not more? If it affects two people so much, surely it'd affect others right? but no, they're all just trophies or passing fancies; the fact one or two want him "more" is set against him having dozens of relationships. None of the other girls are affected (why don't the crazy ones attack them to possess him? why don't more go crazy? what makes his first sexual partners any more important then the others?). It's pretty barmy.
I too am beginning to wonder if we were watching the same show. Firstly, Sekai doesn't really go crazy, she kills Makoto out of anger and despair. Which is understandable considering that he cheats on her; dumps her when he finds out that she is pregnant, but not before blaming her for becoming pregnant and trying to pressure her into having an abortion; and then he makes out with his new girlfriend right in front of her just to drive the point home. Kotonoha on the other hand genuinely does go crazy. She gets tormented constantly by the other girls in her class; gets dumped by the person she loves because he got bored of her; and gets raped all in the space of a few days. Do you not think that this might take a psychological toll on a person? I don't understand how you can ask "why don't more go crazy? what makes his first sexual partners any more important then the others?" You really don't see a difference between these two characters and the other girls that he just has casual sex with once or twice?
I've enjoyed the discussion we've had so far. I'm not really expecting another wall-o-text post in response to this, I know they take a while to write (this one did at any rate).
School Days isn't even one of my favourite shows, I'd much rather have a discussion like this about
Stand Alone Complex or
Death Note tbh but I appreciate the opposing view nonetheless.
tldr; it puts the lotion on its skin.