These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
How many people even realize that that most of the game's endings are very conventional good endings? Including one ending where The Marry Them All solution that is Deconstructed in the anime is played completely straight with Sekai and Kotonoha, now best friends, happily talking to each other like sisters in the snow about celebrating Chirstmas with Makoto by having a threesome and announcing that they are both carrying his children as a present. No Nice Boat here.
A more basic version of this trope would be the notion that the anime came first, or that some fans don't know of the visual novel at all.
Is Makoto just a poor guy who got caught up in the thrill of having so many women willing to sleep with him, that he lost sight of what was really important? Or is he a Jerk Ass who cared for nothing but his own pleasure, and only went back to Kotonoha because she was the only one besides Sekai who would take him? The fact that his Manga Character is VASTLY different from his Anime Character doesn't help.
Also, who does Makoto really like? Does Makoto like Kotonoha truly? Or is it only because of her beauty, while dating wise, he has much more fun with Sekai? At the same time, does Makoto truly love Sekai? Or does he just date her because she lets him do what Kotonoha won't?
In the original visual novel, he's MUCH nicer than in the anime, plus he has a different voice actor in the original visual novel so he sounds less like a jerk and more like a shy boy. But he's not a saint in the visual novel, either: the problem is that his character flaw is different in the game and in the anime. In the anime, his character flaw is that he's a jerk who really likes sex. In the GAME, on the other hand, his main problem is that he's too indecisive and can't make up his mind. And part of what made him so attractive to girls in the game (specifically that he's a really nice guy who once rescued Setsuna from bullies for example) actually works against him in situations where it would be better if he was blunt. So he ends up dating both girls mostly because he doesn't have the heart to break things off for good and hurt their feelings. Which is still a stupid move, but not for as evil reasons as his behavior in the anime.
Sekai. Her reasons and motivations for hooking Makoto up with Kotonoha vary differently between each adaptation. The original visual novel shows her reasons (especially if you pursue her) to be even though she has a crush on Makoto, she genuinely wants him to be happy with Kotonoha who he had a crush on, and that it's Makoto himself who realizes on his own that it's Sekai he wants afterall. In the anime, she's portrayed as wanting to help Makoto, but later implies that she likely had an ulterior motive: that she can get him to like her by helping him get together with Kotonoha. In the manga, she helps them get together but then decides to get together with Makoto behind Kotonoha's back anyway, ignoring the consequences. With each new installment, it seems the creators are going out of their way to make her more and more selfish than before.
Also, there's her behavior around others; in the anime and manga, her pursuit for Makoto can make her willingly try to get others to do things for her and doesn't bother to look at the consequences of her actions or how they affect the people around her. In the visual novel, however, she's more cautious of her actions and it's made clear that the last thing she wants is to hurt others for her sake, such as in the Eternal bad ending she apologizes to Kotonoha for getting between her and Makoto, and in one of Kotonoha's good endings, she seems to be completely unaware of her friends getting Otome's posse to bully Kotonoha, and when Makoto confronts her about it, she's genuinely shocked by it and apologizes for her friends' behavior, even though Makoto ends up breaking all ties with her. Last but not least, there's the possibility that Sekai might also suffer from mental/emotional unstability, though not to the extent as Kotonoha, as her lowest points where she does intentionally try to hurt others are the result of her being subjected to Break the Cutie and Despair Event Horizon, regardless of whether she's shown with the Dull Eyes of Unhappiness or not.
Also, Kotonoha herself. It's strongly implied in some media that she had some degree of mental/emotional unstability, not helped by the bullying she goes through at school and sexual abuse in some paths, and therefore she clings to Makoto because he's the first person outside of her family who seems to want to be with her. However, said "clinginess" can also bring very nasty sides, with at least two VERY bloody bad endings coming from her despair upon being set aside... and yet one of Sekai's paths also state that she can potentially be VERY manipulative, and in Cross Days she can go further and murder persons totally unrelated to the plot, like Yuuki's older sister. Although in this case, Kotonoha was looking for "Yu", and Chie lied saying she was "Yu" so she could protect her brother. The aforementioned manipulative side could also be another result of her mental/emotional unstability. Also, in the infamous "bloody ending", after murdering Sekai, Kotonoha snaps out of her Yandere side and has a My God, What Have I Done? moment, so there might be more to it that it looks at first.
Anvilicious: BOYS, TREAT YOUR GIRL WITH RESPECT. IF YOU DON'T LIKE HER BREAK IT OFF CLEAN. THAT'S THE LEAST YOU CAN DO. GIRLS, DON'T THROW YOUR LIFE AWAY FOR SOME GUY, NO MATTER HOW GOOD OF A LAY HE IS.
Complete Monster: Taisuke evolves into one come Cross Days. He finds out that there is a new "girl" that Makoto is hanging out with named Yuu and stalks "her" until it is revealed that the person that Makoto is banging is Yuki. He blackmails Yuki and forces him as his sex slave, and if he told anyone about it, he would show all the pictures in the school of the type of person he really is, effectively ruining his reputation and thus ruining Yuki's chance of getting Makoto and Kotonoha hooked up together again. He then brings his other friends in on the deal and gang bangs Yuki constantly, and, in one of the endings, it sends Yuki over the edge.
The "Timeless Melody" froms Cross Days which plays on Makoto's best ending, Roka's better endings or Roka's bad ending/ Ai's good ending.
Designated Villain: Sekai can be seen as one in Cross Days. Yuuki's accuses of her seducing Makoto away from Kotonoha, but background events make it clear that Cross Days follows up from the path in School Days that had Sekai deliberately try to distance herself from Kotonoha and Makoto because she didn't want to get between them, and it was Makoto who went after Sekai to express his feelings for her. And since she never does anything particularly villainous in the rest of the story, Yuuki's animosity towards her comes across as misguided at best, and overly cruel at worst.
Yuki for numerous reasons. The main reason is that he's the nice guy to Makoto's jerkass personality and probably the only sane man that is genre savvy enough to realize what's going on. He can call Sekai out on everything she's done to Kotohana and punch Makoto for being a dick. Finally he's the cross dresser that many guys have deemed more attractive than the girls of this series.
Setsuna herself is also one, likely the reason that she get to become the main heroine of both Summer Days and Shiny Days
Don't forget Kokoro! And Itaru!
Fan-Preferred Couple: Surprisingly, Yuki and Makoto. Yuki is the only person that stands up and calls him out for cheating on the girls where Taisuke and his friends praise him for getting multiple girls and "becoming a man". Since at this point of time, he's already in over his head and is out right annoyed that he of all people punched him. However, he falls for Yuki's counterpart Yu because she's different from the other girls he's dated. "She" is the only girl that outright cares that he is going out with multiple woman and because of Yu, he's able to think better and realize the error of his ways. His love for Yu gets to the point where he's willing to stand up to Taisuke for "her". And of course, in the true ending, he shouts at the top of his lungs that he loves Yu. Even when he finds out that Yu is a boy, he realizes he doesn't care about the gender because Yuki and Yu are the same person and Yu changed him.
Fetish Retardant: The second half of the series kicks this into overdrive, like Kotonoha and Makoto french kissing in front of Sekai who starts to have a mental breakdown. \\Some of the sex scenes in the game are rather... awkwardly animated. i.e, sometimes Kotonoha's boobs bounce too much to be sexy, or at times they stay still when they shouldn't.
Why there's no bad ending in Cross Days that Roka or Ai killed Yuuki? One is Yuuki's Nice Guy status. Two is neither girl is as emotionally unstable as as Kotonoha or Sekai, especially Ai, who despite her Mad Love personality, is willing to give up Makoto and Yuuki and let them be happy with who they chose.
Itaru Itou lives with her father Tomaru. The one who already impregnated several of his underage daughters, sometimes with aid of fertility drugs. At one occasion, when she runs away from home to visit Makoto, she tells him she hates their dad - hopefully its only because Makoto is so nice to her, her dad is unlikeable to her by contrast.
Don't know if this help you a little but according to the canonical of Summer Radish Vacation 2, Tomaru was castrated by Rideru Takatsukasa (basically, impotent) so it's likely the latter.
Jerk Ass Woobie: It's easy to feel sympathy for Sekai throughout the story. But considering that her actions were pretty much the reason the entire plot happened. Not to mention that it's even worse in the manga.
Just Here for Godzilla: The bloody bad endings are the main reason why people buy the game. Justifed in that that was intended from the start to be the series primary gimmick.
Hilarious in Hindsight: Possibly the mother of all of them: Daisuke Hirakawa (Makoto's VA) also voiced Will Turner and the way how he ends his story in the films is similar in the same way how Makoto ends his own's... except Will is now the captain of his own NICE BOAT and he does get the girl (and has a kid with her), contrasting how Makoto ends here, when, not only he doesn't get the girl (and their supposed unborn kid either didn't exist or died with her), he also ends in a NICE BOAT... with only his head inside of it.
Makoto: Pick your poison, but one good choice is tongue-kissing Kotonoha in front of Sekai just to hammer the point home that they're through...when she's (apparently) pregnant with his baby!
In the Cross Days manga adaptation, he manages to be an even bigger asshole than the anime made him out to be. Not only he brags about dating both Kotonoha and Sekai with no regards for the former's feeling, he also tries to rape Roka after she decides to confess her feelings to Yuuki.
Sekai: Murder, natch. While Makoto's actions throughout the anime provide for her a Freudian Excuse that makes her actions here more forgivable than those of others in the anime, in the manga she has no excuse whatsoever when she murders Kotonoha without a hint of remorse and even mocks her for calling out for Makoto's help. Or in one of the new bad endings, where she succesfully kills Kotonoha via tossing her in the path of a speeding train in front of Makoto and a huge crowd and laughs about it, while commenting on how it's all Kotonoha and Makoto's fault.
Kotonoha: Double murder (probably), plus the contents of her bag (Makoto's severed head).
And she also has a shocking one in the original visual novel: At one point in the visual novel, Makoto's with Sekai. She seduces Makoto and gets him to promise that if Sekai leaves him, she'll be the only one he'll look at. Next, she takes a picture of them together and shows it to Sekai, while verbally bullying her. This makes Sekai break up with Makoto. That's right, she had Makoto promise her and then purposely upsets Sekai into breaking up with Makoto to make sure that he keeps his promise, thus having him all to herself. And no, Kotonoha has not gone yandere here; this is her being a manipulative bitch and showing that, at very least not in this route, she's not innocent as everyone makes her out to be. Whether she gets away with it or not is up to the player's decisions. If you do have Makoto refuse her, then you get one of Sekai's happiest endings overall.
Taisuke: Raping Kotonoha when she's at her lowest point.
Natsumi, Kumi, and Minami: Taking advantage of a school tradition to tape couples have sex... and then show the footage to the whole school. The victims include their supposed friend Otome, whose feelings they then ignore again by having sex with Makoto just for the hell of it, and Sekai's friend Nanami, who gets taped and exposed by them while having sex with her boyfriend and has her reputation completely ruined among the other students.. The worst part is, in the anime and most paths in the visual novel, they completely get away with their disgusting actions.
In one of the visual novel routes, we also have them cornering Kotonoha, knocking down and stepping over the lunch she made for Makoto with LOTS of effort, and laughing over it. Not only that, but they even plan to treat her worse and at some point corner her to beat her up. Again, depending on your actions, Makoto can stop them, which triggers one of Kotonoha's happiest endings.
Otome: Bullying Kotonoha out of sheer jealousy and in one of the routes, manipulating Taisuke into commiting his aforementioned Moral Event Horizon. If not for her telling him that "girls like to play pretend in sex", he may have noticed that she wasn't willing....
Nanami and Hikari: In the one of the routes, we have them Threathening Kotonoha, and helping Otome and her posse with their bullying of Kotonoha by spreading rumors about Kotonoha being a "pheromone girl", and also the ones who tipped the 4 of them about Kotonoha's lunchbox so the could step over it as mentioned above. And they also plotted to have the entire sports club help them make Kotonoha even more miserable. All to drive her away from Makoto so Sekai can be with him. It backfired spetacularly on them, however, in which, should Makoto choose to stop Otome's posse from bullying Kotonoha, Makoto goes Tranquil Fury on all of them before cutting all of his bonds with Sekai.
Even worse, if Makoto never finds out about the bullying, it leads directly to the infamous "Bloody End," where Kotonoha murders Sekai in broad daylight.
The entire idea of cutting open someone with a butcher knife to check to see if she's pregnant will likely be completely laughable to those who don't find it completely disgusting.
High Octane Nausea Fuel: The anime's finale. Sekai stabbing Makoto to death was one thing. Kotonoha cutting off Makoto's head, stuffing it in a bag, and showing it to Sekai was another (then cradling it on a Nice Boat) was another thing. The High-Pressure Blood from Kotonoha killing Sekai was yet another. But Kotonoha cutting open Sekai's uterus to confirm whether she was pregnant... Wasn't like I was planning to eat...for the next few years or so...
Never Live It Down: The original visual novel gave the characters complex motivations and had most of them at least trying to act rationally, but since the anime and the manga expand on the worst endings possible, anybody who knows of the series will always know Kotonoha and Sekai as a couple of psycho love-stricken bitches with Makoto as the idiot in between whose actions sparked the flames.
One True Threesome: The "Two Lovers" ending has Makoto together with both Kotonoha & Sekai, all on good terms with each other, and just in time for Christmas.
Makoto's manga incarnation, as well as in the OVAs. He remains an idiot in these incarnation, but is also quite less of a Jerkass and does care for the girls.
Playing the original visual novel video game after having watched the anime may also contribute to the rescuing. He's not really a jerk in the original game either when compared to his anime self. (He has a slightly nicer voice in the game, too.)
While the hatred towards Makoto and Sekai may be understandable to a degree, it's really blown out of disturbing proportions, with Sekai having it worse. Yes, they both have their flaws that can in ways affect the story, but people very often ignore their positive and/or redeeming qualities. One common reason is that most fans have seen the anime first and immediately transfer those portrayals onto the visual novel counterparts, biasely treating them as horrible people from the very beginning while treating Kotonoha as a Purity Sue, forgetting her flaws that can make her just as horrible as the other two.
Also, Kotonoha herself. Some people seem to ignore Kotonoha's positive qualities and blow her Yandere traits out of proportion, ignoring the fact that she's constantly subjected to Break the Cutie and that she only shows her Yandere traits on the bad endings. Outside of them, and one route where she shows a meaner and more manipulative side of her, she's easily one of the nicest female characters of the series.
Kotonoha goes murderous in "Bloody End" as well as the path that leads to "With Kotonoha", "To Kotonoha", "Love Fulfilled", and "Earnest Feelings Requited". She goes out of her way to traumatise Sekai in the path that leads to "I Love You" and "Forever" as well as the path that leads to "Bavarois" and "Lust", and her actions along the path that leads to "Two Lovers" and "To My Child" are rather unsympathetic as well. That's over half the endings the game has. She's not a completely irredeemable yandere on the level of Gasai Yuno, but to characterise her as mentally unstable is entirely reasonable.
The two heroines of Cross Days, Roka and Ai suffers this as well. With Roka being targeted because of her routes is too "straightforward"(despite that it's very likely intentional as Yuuki is true to his name in those routes instead of resorting to somewhat more manipulative ways in Makoto's routes) while Ai's because of her willingness to break Makoto and Kotonoha aparts and get pregnant with Yuuki's child and her Mad Love status which fans seem to disregard that it's partly Yuuki's fault(which he decide to take his responsibility of in "Only Love and Courage") or that in true route she decide to not blame it on Yuuki and lets him be happy with Roka.
All above hatedom is really nothing compared to Tomaru Sawagoe's hatedom. Seriously, that guy is only for sex and money and his crimes are much worse than everyone else combined. In summary:
Using Tomoe's affection toward him to have access to her fortune.
Was responsible for one of his daughters' death due to underage pregnancy.
Doesn't treat any members of his harem like human being.
Drugged (and almost certainly raped) his daughters so he could impregnate them when they were as young as FIVE.
Kotonoha's response to being dumped is perhaps a tad overdone. Then again, she might have had some mental disorder to start with.
Further on the mental disorder topic, Kotonoha is also the one who suffers the most Break the Cutie moments in the series, in all adaptations, be it from bullying, being betrayed, excluded, threathened, dumped or raped. Even someone not as insecure and shy as Kotonoha is would have some serious emotional damage from all that.