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.
Alternate Character Interpretation: Kohaku probably lends herself to this more than any other character. How much control does she have over SHIKI/Roa's actions? Is she drugging everybody, and how often? Does her backstory excuse her actions? It's made worse by the fact that the answer to any of these questions, and more, could be answered quite differently depending on the route. Makihisa Tohno also lends himself to this, though it's mostly along the lines of whether he's truly a monster or something less, due to much of his villainy being in response to factors beyond his control.
Anticlimax Boss: Roa / SHIKI. The game made you think that he is a truly Bad Ass enemy that even Arcueid knows isn't an easy opponent or made Akiha increase her powers in order to destroy him. When we have the Shiki vs. Big Bad fight, what happens? Shiki kills him with very little effort. I know that Shiki's eyes are the killing weapons, but still...
Justified in Hisui's route since SHIKI was undergoing a Villainous Breakdown from killing his blood sister Akiha and had been severely weakened in his earlier fight with her. After the death of his only close relative by his own hands, its possible that at that point SHIKI was hoping to die.
'Justice' (the song playing in the background during the Shiki/SHIKI fight in the anime) is not half-bad either.
Ensemble Dark Horse: Nrvnqsr "Nero" Chaos and Satsuki "Sacchin" Yumizuka seem to be well liked, with the former due to his badassness and the later for her cuteness and unfortunate fate both in-game and metawise.
Fan Nickname: "The Tohno Gland" (Shiki's ability to attract women no matter what he does - fans joke it's pheromones).
It would be more correct to say "Nanaya gland" though since he is biologically a Nanaya. However, since it's just a joke it doesn't really matter.
Once you go through Hisui's route and learn the truth about Kohaku everything involving her becomes very, very cringe inducing.
Also, during the climax of Akiha's route, fearing that she will invert, she asks Shiki to give her a Mercy Kill if she ever inverts. Shiki refuses to do it and the ending of her route depends if he goes through with it or not. It becomes harsher once you read the manga and realize that little SHIKI asked Shiki to do the same thing and the Foregone Conclusion of it makes it harder to watch.
Once you read the manga, Drinking Dreaming Moon becomes this too.
Arcueid and Ciel, despite their attempts to kill each other, are actually Vitriolic Best Buds. Not to mention that official Take Moon Manga, when Arcueid gets drunk and starts fondling Ciel's butt.
Neither Shiki nor Arihiko use Honorifics when talking to each other, but it's Shiki's habit of also referring to Arihiko by his first name (a habit usually attributed to girls) that makes Akiha do a double take.
Also, Shiki and SHIKI were apparently very close as children (which is confirmed in the manga), so much that Akiha was jealous of them.
Some Les Yay with Kohaku and Akiha was only made worse(or rather, better) in the anime. Kohaku's back being turned means the scene with Akiha sucking Kohaku's bloodlooks ahelluva lotmore questionable.
...that's pretty much impossible, since the game's CG rather clearly shows Akiha sucking on one of Kohaku's naked breasts. It was actually less explicit in the anime.
That CG also shows specifically that Akiha is sucking Kohaku's blood. The anime being less explicit means it looks more like she's suckling.
It Was His Sled: Most newcomers to the series know all of the spoilers that are supposed to be surprising twists, because of the amount of side-stories and sequels written for the game. 1. That Shiki is really the adopted son of the Tohno family. 2. That SHIKI exists. 3. That Kohaku and Hisui switched roles and Kohaku is actually a Stepford Smiler.
Nightmare Fuel: So, so much Nightmare fuel. Help me. Help me. helpmehelpmehelpmehelpmehelpmehelpmehelp me. I should just become a doll.
All routes have insanity creeping into Shiki's head at some point, but the entire middle part of Hisui's route sees the protagonist immobile, in bed, gibbering unintelligibly as he descends into several different kinds of madness simultaneously. You're playing a game from the perspective of a character who is desperately, vainly trying to cling onto the tattered wreckage of his personality; afraid to be awake for fear of what he'll do to the people around him; terrified of going to sleep because of the murderous dreams that invade his mind; all the while tormented by agonizing migraines and uncontrollable bouts of furious rage...
And the very worst part of this is when, locked in the throes of madness, you see Kohaku's true smile for the first time.
which isnt helped by Kohaku masquerading as Hisui at the time.
The manga, by virtue of being illustrated, shows off much better why Shiki's Mystic Eyes nearly drove him insane at first. Having the entire hospital, and especially all the people in it, covered with the lines makes them look both incredibly fragile and freaky as all hell.
Also from the manga, we get a depiction of what happened to Ciel after she revived from being killed by Arcueid wile possessed by Roa. Bascially, the Church attempting to 'correct' as what they saw as an unnatural body, had her killed at least six hundred times including such deaths as by drowning, burning and organ removal, the whole time as she begged them to stop, only quitting when they decided she'd be more useful as a Burial agent. Afterwards, Ciel is shown as completely broken and resigned.
To be fair, Neco-Arc was probably embellishing a little bit or outright lying - especially on the cannon. But Satsuki does seem to be listed among the heroines in the Enhanced Remake coming out, so the truth might soon be there...
Squick: In order to hone and maintain the Psychic Abilities within the family, the Nanayas practiced a heavy system of inbreeding which resulted in severely deformed individuals
The Woobie: Oh where to start? There's all 5 main heroines to start with. Then there's Len, Sacchin, and Nanako. But above all of those is the real Tohno SHIKI. Not Roa, SHIKI. Just think about his life for a second, you'll see it.
Becoming the monster he is now can be blamed on at least three things beyond his control, a combination of his particularly strong awakening of the Tohno's demon blood, being the 18th reincarnation of Roa, AND being locked in a basement for years while Kohaku drugged him and generally fucked with his mind. He didn't really have much of a chance.
The side-story game Kagetsu Tohya gives a small amount of closure to this with the final, hidden Tear Jerker bonus story "Drinking, Dreaming Moon" where Shiki and SHIKI finally meet on friendly terms in a dream.
Shiki has had more than a few traumatic experiences in his backstory too. Getting kicked out of his home by his father for having a near lethal injury that made him see death everywhere is only the beginning, and that's not even getting into the more spoilerrific elements of his backstory. Though to give an example of one of those bits, the opening scene, before the hospital? That's his entire blood related family being slaughtered right before his eyes. He's remarkably well adjusted in spite of it.