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.
Alternative Character Interpretation: Practically every single character is left slightly insane from their troubled pasts, or completely evil. Often it's very hard to keep them apart.
Humans Are Bastards needs to be taken with at least a grain of salt; The researchers and staff on the island definitely call their essential Humanity into serious question. But the vast majority of people in Japan and on Earth had no say in how these girls were treated, and never even heard of them until the war Kouta describes in the manga finale took place. As has been pointed out elsewhere, the age these girls get their powers makes their misuse inevitable. So, while prejudice must be condemned, the first time people even hear about Diclonius is when their neighbors' three-year olds kill them. Much like in X-Men or the various Devilman series, ordinary Humans aren't offered a lot of choice on how to view their potential replacements. This said, many non-Kakuzawa-employed Humans in the series do not acquit themselves terribly well.
Even some of the researchers get called into question. Several signed up because the Diiclonius births killed family, or rendered them unable to bear children. Some go For Science!, like Nousou, and quite a few don't want to disappoint The Director. The Operative at the end clearly hates Lucy for killing those near to him.
Saito in the Manga, did she really love Mariko? She manipulated her into thinking her father hated her, but before that, she repeatedly expressed excitement over finally seeing her, after speaking to her for years and helping to raise and educate her, she admits to feeling a sort of bond with the girl.
The Other Facility, because we know so little about it. Of the Four characters we meet from there, only Shirakawa is named, The Agent and the two Operatives go unnamed. We know its purpose is vector research, and they're monitored more closely by the Japanese Government, but we don't know if they have an agenda, want to save the world, or solve the problem to prevent Japan's implication in dooming the planet.
The "Unknown Man" in the manga. In order to find our protagonist, he crafted a radar system made from a silpelit who was still alive, by cutting her lower half. In order to make sure that she wouldn't use her powers against him, he also built a tank for her which would keep her in a constant state of excruciating pain. He also felt it would be a shame to let said diclonius' body go to waste, so he, in no grey terms, raped her before he cut her legs. Finally, just when you think this guy couldn't get any more repulsive, he attempts to rape Mayu.
Mayu's stepfather. He is a child molester who loved to sexually humiliate her, and it's shown he went as far as to sodomize her. He gets no comeuppance for this, as he's only shown in flashbacks.
The Lucy hatedom gets pretty rabid too, but how much of this is Die for Our Ship and how much is simply hating Lucy because she's a villain is completely impossible to determine.
Ear Worm: The opening is probably one of the biggest Ear Worms in anime history.
Ensemble Darkhorse: You'd think such a series has no fan favourite character, considering everyone is either mentally broken or outright villainous but nope, one of the most popular characters outside the main cast is Kurama. Suprisingly, about as much liked is his daughter. Yes, the psychotic tragic villain Mariko.
Esoteric Happy Ending: The final chapter of the manga clearly states that the World Health Organization "forbade" the birth of Diclonii worldwide until they discovered a vaccine capable of preventing their conception. Red tape and technobabble aside, the term for this is genocide.
Fanon: The Unknown Man is thought to be a Kakuzawa and thus is related to the Director. They do know each other, and the Unknown man does seem to know and support the Direcotor's agenda. However, they are never confirmed to be related, and it's unknown if the Unknown man wears a Hairpiece to disguise little horns on his head.
Fridge Brilliance: Lucy frees Mayu's puppy because her puppy was beaten to death when she was younger.
This is a more minor case, but Mariko's four viable clones are named Alicia, Barbara, Cynthia, and Diana.
Lucy's real name is Kaede. It was right in front of us the whole time: The main characters live at the Maple Inn.
Germans Love David Hasselhoff: The show didn't get very far in Japan (partly due to being hardcore enough that it couldn't be broadcast on-air even in Japan), but was a major Sleeper Hit in America through DVD sales. Same for the actual Germans.
Hype Backlash: It's one of the few series 4chan users refuse to talk about due to this reason.
As said before, Nyuu is a girl with the body of a 18 year old and the mind of a 2 year old and as a result has no inhibitions at all. Kouta knows how to keep her in check quite well, but when he's not around she practically sexually assaults a number of the other girls in the house.
Later in the manga, after being Nyu for a long time, Lucy at one point looks at Yuka and is puzzled why she is feeling compelled to grope her.
The Inner voice is also subject to this, is it the root of her DNA speaking to her? Is it another personality that formed through all of the abuse breaking her? Is she the Embodiment of the Diiclonii? Or is she some combination of all three.
Brutally murdering Kouta's father and little sister without any provocation was so horrible and over the top that, even when Lucy became The Atoner, plenty of fans thought that there was no atonement for that.
Others also add slicing off Nana's limbsafter the threat she posed was completely neutralized.
And for some, trying to kill Mayu after Mayu tried to help her.
Ron the Death Eater: Now, Lucy is clearly not innocent by any measure. However, to go along with the Fan Dumb, there's the Hate Dumb that think of her as nothing but a pure evil person who would always kill others For the Evulz as soon as something goes wrong. Now granted, she certainly has shown this behavior early in the series (examples shown above), but as the story goes on (and definitely more prominent in the manga) it shows that she does feel guilt, remorse, and regret for killing, and does try her best to NOT kill anymore and would've been content to live with Kouta and her friends with no longer having to kill. However, the people of the Diclonius Research Facility always keep screwing her over and over, and forcing her back into killing people, making it difficult to nearly impossible for her to atone and any hope she can find in humanity and a better future grow dimmer each time. And she's being manipulated by a Split Personality that represents her innate diclonius instincts, which she first tried to suppress. Seriously, the girl just can't win.
Angst Dissonance: One of the biggest non-shipping reasons for her becoming The Scrappy, being one of the most well-off characters in the series, but complaining about her unfortunate circumstances more than any of them.
Lucy/Kouta fans LOVE to bash Yuka for being clingy, despite Lucy also being clingy in other (and scarier) ways. It makes you wonder if those fans really appreciate the Lucy/Kouta pairing for how screwed-up it actually is in canon...
People in the West bash her since they're both cousins, and incest of any kind is largely taboo and considered "disgusting".
Hollywood Homely: When she's first introduced she is described as looking like the homeless child she has been for perhaps several weeks at that point. Problem is, virtually nothing about her physical appearance suggests this.
Jerkass Woobie: He's an asshole, yeah. But he still manges to come up as more decent than others assholes here.