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.
Also to a less extent Masao, established as a petty, hateful character from day one whose only redeeming quality, his reluctance to feed on living humans, is rather spoiled by the fact that it's more due to cowardice than any noble conviction. However, one feels at least a bit of pity for him when he ended up dying at the hands of his own half-sister after thinking he'd made it to safety. Although, given his rather unwarranted spite towards her when alive, one could also argue that this qualifies as a Karmic Death.
Given how much nastier he comes across in his death scene in the manga, it's pretty clear the anime was gunning for this trope.
Fashion-Victim Villain: It seems that the more serious Shiki gets, the odder the costumes are. Near the end of the series, Chizuru wears an outfit that looks like it's made out of strips of red tape, Tatsumi wears a very unfortunate one-piece hoodie with unbearably short shorts, and Sunako appears to be cosplaying as the Queen of Hearts. Even Natsuno gets fashionably challenged after becoming a Shiki (his pink sneakers are just the start of it).
Ho Yay: Tohru and Yuuki have plenty of this at the start. It becomes even more obvious after Tohru becomes a vampire, Yuuki is willing to risk his life in order to convince Tohru to escape the town with him. The pairing is quite popular among fans, only second to Toshio/Seishin, another pairing that gets some Ho Yay moments of their own.
Idiot Plot: When going over all the symptoms, exhausting themselves trying to work out what is killing everyone, they somehow never draw the connection that the only thing every single victim has in common are bug bites.
Les Yay: There's a little Ship Tease between Kaori and Megumi, and the pairing has a small following as well.
Moral Event Horizon: Toshio performing vivisection on his newly-turned shiki wife to figure out what the Shiki react to.
Later in the manga Toshio leading Chizuru on, betraying her, and killing her in the most brutal way possible. The villagers didn't help either. One of them threw a giant rock at her head and caused blood to pour out of her eyes. OUCH.
In episode 20 the villagers go as far as to kill humans simply under hypnosis. It gets worse in episode 21 where Ookawa's group murders Seishin's family thinking they're involved with the Shiki.
It gets even worse in 20.5 where they kill people who have just been bitten and were not hypnotized out of fear of them turning into Shiki.
The Shiki are hardly innocent either. Sunako masterminded the plan to turn the village into a haven for Shiki, fully endorsing the mass murder of the population in the hopes that some would rise from their graves.
Agreed. The Shiki were the ones who murdered people and encouraged any newly 'born' Shiki to go and feed on their own families. Especially since as Dr Ozaki proved, it took three feeds to actually kill a human. Why couldn't the Shiki keep rotating around the village and waiting for blood supplies to replenish?
Because the Kirishikis are the ones in control of them and they want the village to become a haven for Shiki. Which requires that they feed on everyone to they die. Regardless of whether the other Shiki want to. Shiki who defy them can have things end up bad for them such as being tied to a tree to burn during the day and Tatsumi mentions in the manga he wants humanity and Shiki to wipe each other out.
The Werewolf who turned Sunako despite the fact that he doesn't need to feed on people to survive and Sunako's family who kept sending her maids to feed on also crossed it.
Megumi crosses this when she kills Tohru out of jealousy or killing her best friend's father out of pure spite.
Dr. Ozaki's research on his recently risen wife to find out what makes the Shiki tick. He cuts her open and torments her with religious icons before finally staking her... and he does it all without showing any real emotion.
Masao as a child◊ was so creepy he managed to freak many fans out even more than the vampires.
The Scrappy: Masao for being a whiny and self-centered teenager, and Megumi for being selfish and sadistic.
True Art Is Angsty: This extremely dark, depressing show all about exploring the dark side of human nature and presenting just how futile and pointless death can be has received lavish praise from most reputable critics and the vast majority of people who have seen it in some form.
Ugly Cute: Masao to some; possibly a few other characters as well.
The ever heated internet argument about what is truly Shonen or Seinen will never die, but is almost accepted that monthly shonen manga will be more lax about showcases of detailed violence and sexually suggestive themes to the point of nudity.
The anime, though, was run in an adult programming block in Japan—and the Funimation release is rated TV-MA.
The Woobie: Where to start? It'd probably be easier to list characters who didn't qualify!