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 Christmas 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 Jerkass 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.
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, and 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 after all. 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 instability, 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.
Sekai may be harder to understand in the visual novel due to the inconsistency of her actions. On one hand, she forcefully kisses Makoto at the end of the first episode (something that is completely out of the player's control). Later, she can offer to let Makoto practice kissing on her; something that inevitably leads to intercourse. Whether she was intentionally using "practice-kissing" as an excuse to get into Makoto's pants or she just got carried away in the moment, she was a key player in Makoto cheating on Kotonoha.(It should be noted that Makoto can be the better man in this instance and turn her down.) On the other hand, she will distance herself from Makoto so he can be with Kotonoha; and because of the numerous branches the player can take, this presumably can happen even on routes where the aforementioned "kissing-sex" takes place. She can also turn violent and kill Makoto/Kotonoha in a fit of jealousy and/or vengeance. Really, she is, at best, someone who is just as indecisive as Makoto is and lets her impulses and emotions control her actions, or, at worst, she's an unstable sociopath who is in a perpetual HeelFace Revolving Door.
Also, Kotonoha herself. It's strongly implied in some media that she had some degree of mental/emotional instability, 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 people 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 instability. 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.
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.
Ass Pull: In the anime, Hikari Kuroda has a one sided crush on Taisuke Sawanaga, but she is too shy to directly confess her love for him. However, despite the fact she's never shown any interest over him, and she even punches him when he thought that she liked him, she starts fucking Makoto behind Sekai's back.
Best Known for the Fanservice: If someone isn't playing the game for the memetic bad endings, they're probably playing it for this (it is an eroge after all). US publisher Jast USA knows this, as they included a 3D mouse pad with the Collector's Edition of the game (i.e. they included a mouse pad that features Kotonoha with 3D breasts).
Broken Base: The divisive reactions may often be simple at first glance but arguments against each other camp are several. Namely, there are those who like the anime adaptation versus those who hate the anime:
Some like School Days due to its Deconstruction of the Harem Genre anime that were prevalent before it, making it one of the few unique titles that put some darker twists to make it stand out. Specifically, having the Anvilicious messages about having only one true relationship and falling for the right person, that having multiple partners in real-life will have severe consequences (mentally or emotionally) from all involved individuals. Others point out that the consequences of the characters' actions (i.e. being secretly caught having sex and humiliated for it, being depressed about pre-marital pregnancy, being traumatized by a boyfriend cheating on you, to outright "murder from passion") are things that may actually happen in real-life. Therefore, the anime makes a good attempt to portray the realistic consequences of having multiple partners at once.
Some hate the anime mainly due to the Idiot Plot presented, where characters in general were so "poorly-written" they could have at least sorted things out by communicating openly, but they don't until it spiraled into a whole mess. This goes also with fans stating that the characterizations are either bland, overblown or unexplained (which lead to Alternative Character Interpretation) - Notably Makoto only being obsessed with his lustful instincts that it overtakes his reasoning, or that his actions only make more problems than solutions. Others didn't like Kotonoha acting so obsessed with being one man's girlfriend that she doesn't even doubt his actions even by a little bit for the majority of the show. Some question Kotonoha's extreme obsession throughout most of the early episodes because her Yandere trait only surfaced on the latter parts of the anime. Then there's also the Ass Pull situation wherein Hikari decides to have sex with Makoto despite not having any hints of romantic feelings towards him before, or the Narmy voice of Saionji in some parts.
Catharsis Factor: Makoto's depiction in the anime had viewers label him as the worst written Harem protagonist who is only drived with his pleasure, while his constant switching of partners mid-way and breaking up with Kotonoha also drives more hatred into him, especially for fans of Kotonoha. That being said, viewers were likely glad that he is killed at the end of the anime, stating that Makoto got what he deserved for being such a playboy.
Makoto's Jerkass behavior. While it is possible to make him a Nice Guy by treating Kotonoha and Sekai right, the Bad Ends are a result of him treating one or both of the girls terribly. Unfortunately, his negative traits are transferred over to the anime where there are fans who loathe him and were glad that he was killed off by Sekai.
Same with Sekai. She initially seems willing to help Makoto in wooing Kotonoha, but then she decides that she wants him for herself. Many fans blame her for Makoto's downward spiral into his sexual adventures.
The anime as a whole can make you feel this way, especially as it reaches its climax. By the end, there is not a single character who is not loathsome in some way or the other. Kotonoha is probably the most sympathetic as, up until the last few episodes, she is never overtly malicious to anyone, while everyone around her treats her pretty horribly. However, the extent of her violent Yandere behavior at the end more or less erases any sympathy you might have for her.
Designated Villain: Sekai can be seen as one in Cross Days. Yuuki 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.
Die for Our Ship: Even though the original game is known for having literal death scenes from the several Multiple Endings, there are debates among the fandom regarding which girl(s) should have canonically died for Makoto to be with only one partner in the end, most of which use the anime adaptation's characterizations as the basis. Kotonoha fans Vs. Saionji fans Vs. Setsuna fans are the most common.
Yuuki 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 realizes 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 the children Kokoro! And Itaru!
Fan-Preferred Couple: Surprisingly, Makoto and Yuuki. Yuuki is the only person that stands up and calls Makoto out for cheating on the girls whereas Taisuke and his friends praise and envy him for getting multiple girls and "becoming a man". At this point in time, Makoto's already in over his head and is outright annoyed that Yuuki, of all people, punched him. However, he falls for Yuuki's alter ego "Yuu" 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 girls and because of "Yuu", he's able to think better and realize the error of his ways. His love for "Yuu" gets to the point where he's willing to stand up to Taisuke and his thugs for "her". And of course, in the "Only You" ending, even when he finds out that "Yuu" is a boy, Makoto realizes he doesn't care about the gender because Yuuki and "Yuu" are the same person and "Yuu" changed him. The fact that Yuuki's not already related to Makoto or otherwise mentally unstable doesn't hurt, either.
The second half of the anime kicks this into overdrive, like Kotonoha and Makoto french kissing in front of Sekai who starts to have a mental breakdown. At least some of this may have been intentional.
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, and in Cross Days the scene where Makoto does Hikari reverse cowgirl style is damn hilarious because the animators can' decide whether Hikari has her bra/shirt on or not during the sex.
The knowledge that Makoto is closely related to most of his love interests via their descent from Tomaru Sawagoe and his incestuous relationships makes a lot of the H-scenes extremely squicky in hindsight.
Hilarious in Hindsight: 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.
Not only is School Days well known for its bad endings, but even searching for the title online will lead to a lot of spoilers and giveaways, particularly the ending of the anime will pop up more often in forums, discussions, or image results.
Due to it becoming a meme associated with this title, even searching the "Nice Boat" phrase online will also immediately spoil the anime's Wham Episode to those who haven't watched it yet.
Les Yay: Aside of the Sekai/Kotonoha fondling and kissing from the Three-Way Sex scenes in the original, Cross Days has a scene where Makoto has sex with Hikari... while Roka fondles and then does Nanami.
Just Here for Godzilla: The bloody bad endings are the main reason why people buy the game. Justified in that that was intended from the start to be the series primary gimmick.
Memetic Mutation: "Nice boat." In fact, the meme was such a hit that the creators of the original game sold Nice Boat related merchandise at a past Comiket event. The remake also made a new meme out of four PS2 endings. "Nice TRAIN".
For some reason, people didn't take the seriousness of the drama and murders all too seriously. And the creators are perfectly okay with laughing at themselves too, or so it seems.
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.
Sekai's voice tends to be hit-or-miss. When it hits, it creates powerful moments like that heart-wrenching scream after Kotonoha and Makoto make out in front of her. When it misses, it's this trope in full force — because she sounds like a squawking bird.
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 (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...
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.
On the VA front, it took a while for Daisuke Hirakawa to live down being the voice of Makoto, one of the most hated protagonists in anime.
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, treating them as horrible people from the very beginning while treating Kotonoha as ideal, 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, although she shows a great deal of manipulative meanness to get Makoto in some of the routes, she's easily one of the nicest female characters of the series (even if that's not much of a horse race.)
Shocking Swerve: In the manga, the girls' emotional breakdowns, culminating in Kotonoha trying to kill Sekai and Sekai killing Kotonoha aren't as built up as in the anime.
Special Effects Failure: Simply put, the visual novel, particularly during H-scenes, recycles clips and motions that lead to shed clothing reappearing seconds later, mouths moving when no words are being spoken, and frames being inconsistent with the subject of the scene. Once you notice the inconsistency in animation, on top of the occasional Off-Model such as eye shapes, it kills immersion because you can't stop thinking about it.
Wangst: Kotonoha's response to being dumped in some of the routes can come off as a tad overdone for some players; while she can go through a lot of Break the Cutie moments, and no matter what is the subject of harsh bullying, it's hard to keep that in mind during the actual moment.
Watch It for the Meme: The "Nice Boat" meme has become attached to the anime to the point that there are those who watch the anime solely just to understand the context of the meme, and also for the shocking Bad End.