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.
The theme that Humans Are the Real Monsters 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.
Is Big Bad Director Kakuzawa truly meant to be seen as a brilliant manipulator with tons of gambits running to his favor? Or is he meant to be seen as a parody/deconstruction of this, since his plans involve letting his enemies know he's doing it without covering every angle someone could use to undo them, taunting his 'Queen' with how he raped her long-lost mother who it turned out always loved her, and creating a replacement race that was 99.9% sterile, among other things? Were these plotholes, or does the depths of his evil and the successes he does have fool the reader/viewer into thinking he's all that?
At the end of the manga, Lucy's extremely misanthropic hidden personality takes over her body as it breaks down, attempting to have its now global-spanning vectors take out humanity before it dies. When Kouta can't bring himself to shoot her, despite both Lucy and Nyu's personalities begging him to do so, the DNA Voice suddenly stops, puts the gun back in Kouta's hands, and asks for a Mercy Kill. Was it really just in too much pain to continue its genocide, or did it rethink its view on humanity upon seeing that Kouta wouldn't shoot her even when she was trying to eradicate the human species? Or did the other two personalities join together to force her hand?
In response to his Trauma-Induced Amnesia, is Kouta a good kid that honestly doesn't believe that Nyu could harm anyone or someone who goes past the point of believable denial and refuses to see the obvious evidence?
Angst Dissonance: One of the biggest non-shipping reasons for Yuka 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, especially when it comes directly at the expense of one of the worse-off characters, typically Kouta.
Base-Breaking Character: With all of the actions and deaths Lucy causes in the series fans are divided. How sympathetic she is vs. how much the manga wants the reader to sympathize with her is a main sticking point. Fans either view her as one of the best examples of a Jerkass Woobie whose harsh life and trauma are played against all of her atrocities or they feel that the manga tries to wring out much more sympathy for her than she deserves.
Captain Obvious Reveal: Seriously, who didn't figure out Lucy killed Kouta's father and sister before it was revealed?
Complete Monster: The unnamed hitman is a sadistic, pedophilic monster hunter. To find Lucy, the hitman mutilates, then rapes, a silpelit diclonius, leaving her powerless and without her vocal cords to be used as a radar system. Hunting for Lucy, the hitman tries to rape her human friend, the defenseless teenage girl, Mayu, disgusting even his fellow Blood Knight hitman, Bando.
Creepy Awesome: Lucy and Mariko are utterly vicious, but that's why they're so effective.
Critical Dissonance: Critics generally give this series negative reviews, and mixed ones at best, citing excessive gore and nudity which they regard as exploitive and criticizing some of the characters as being highly simplistic, bland, and/or hard to relate with. The closest any professional critic has ever come to giving Elfen Lied a positive review was as being So Bad, It's Good. However, as one can tell under the Cult Classic and Germans Love David Hasselhoff entries, audiences view it far more favorably.
Cult Classic: In Japan at least. In America it's one of the most well-known anime series, being called one of the "classics" by several people.
The Lucy hatedom can get pretty rabid, 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.
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".
Ear Worm: The opening is probably one of the biggest Ear Worms in anime history.
Ensemble Dark Horse: You'd think such a series has no fan favorite character, considering everyone is either mentally broken or outright villainous but nope, one of the most popular characters outside the main cast is Kurama. Surprisingly, 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.
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 Director'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.
Some of the Diclonii eventually survived the year; The twins' ethnicity at the end of the manga is left ambiguous.
One piece of Jossed Fanon is Nana being the younger sister of Number 3, the Diclonius who infected Kurama; this appears to be misinformation repeated verbatim across the net, and unsupported by either version of the series.
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 and especially for Mexicans, to the grade a full orchestration of the anime's OST was performed in Mexico City.
Harsher in Hindsight: The prospect of Lucy massacring citizens left and right became more heartbreaking after the Akihabara massacre occurred in 2008.
Hollywood Homely: When Mayu is 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.
Be ready to feel the urge to sock her in the face... just before giving her a hug. That's Lucy in a nutshell.
Bando is an asshole, yeah. But he still manages to come up as more decent than others assholes here, which makes some of what he gets put through thanks to the other assholes rather difficult to watch.
Love to Hate: Manga only. Director Kakuzawa is a fairly despicable character but undeniably a darn good villain.
Nyu is innocent and nice and friendly, and gets additional points for her being a cute mute. All of these traits are underscored by her contrast with Lucy. She loses some of these traits in the manga when she learns to speak and behave properly, but remains adorable.
Nana too, in her own way, is cute as a button even with less childishness than Nyu.
Lucy's bullies crosses it when they murder her dog. Lucy crossed it when she murders Kouta's family. Mayu's stepfather crosses this when he sexually harassed her. Her mother crossed it when she didn't stop him. Anything Kakuzawa and the Unknown Man do.
While fans are split on whether or not Lucy herself crosses it, everyone agrees that her DNA Voice personality crossed it when she manipulated a broken Lucy into the aforementioned atrocities she commits. If that wasn't enough, then it attempts to destroy the planet in her dying breath out of spite that she won't get to rule a Diclonii-only world.
Due to the over-the-top art, a lot of the gory scenes end up looking more cartoony than intended. Less so in the anime, but it compensates by making the blood spatters that much more over-the-top.
The constant nudity and Fanservice can turn otherwise serious scenes into this.
This whole series is supposed to be a sort-of lecture on how "Humans Are Bastards". Only that the "humans" (save for Kouta and his family, Mayu, Yuka, Nozomi, Arakawa, Kurama and later Bando, and in the past Hiromi), and by the end Anna Kakuzawa and possibly the Agent too, tend to be so obviously, ridiculously, flatly, and STUPIDLY evil that the emotional impact is completely gone. Nevertheless, this actually works a lot of the time, but it's still a bit hard to swallow that most of the human cast is this one-dimensionally villainous.
The most notable example of this is Tomoo and his gang during the infamous scene where they beat a dog to death. This was the cartoonishly psychotic behavior coming from a ten-year-old boy that often got spoofed in Jojos Bizarre Adventure, and yet was played completely straight here.
It's impossible to see the early fight between Nana and Lucy and not immediately think of the Black Knight scene.
Rescued from the Scrappy Heap: While a few people find his anime counterpart amusing in some cases, most would agree that Bando has little to no redeeming factors and would rather have seen him killed by Lucy than spared. His manga counterpart has much of his jerkassery toned down considerably, given multiple moments of character development and badassery and is widely considered to be one of the best characters in the manga.
Lucy manages to be an odd case that's a victim of this, along with Draco in Leather Pants. Now, she clearly isnt innocent by any measure. However, there are some that think of her as nothing but pure evil who would always kill others as soon as something goes wrong, just because. Now granted, she certainly shows this behavior early in the series, but as the story goes on, it's made plain that, yes, she does feel awful over what she's done, and does try her best to NOT kill anymore and would've been content to live with Kouta and her friends. 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.
Yuka gets this the most. Lucy/Kouta fans seriously flanderize her Clingy Jealous Girl tendencies to Scrappy levels to make room for Lucy to kill her and win Kouta's affections, even though in canon, killing Yuka is the last thing that would win Kouta over to Lucy.
In some cases, Kouta himself gets this treatment due to fans who view the mistakes he made as a kid (mainly lying to Kaede about both his cousin's gender and that he'd go with said cousin to the festival, and especially slapping his little sister in anger) as Never Live It Down moments for him.
Squick: Nyu's face when groping arouses her. Likely due to the high amount of tears gushing out of her eyes, it makes the reader feel very uncomfortable.
They Wasted a Perfectly Good Plot: Kouta's lack of memories of his time with Yuka puts a damper on their potential of reaching a decent relationship, though Kouta has good reasons for it. Yet, when he eventually regains his memories of Lucy killing his sister and father in front of him, he focuses more on snapping at Lucy and simply telling her that he 'can't forgive her', when this could have been a great opportunity to also have Kouta remember his moments with Yuka, how he loved her since childhood and get the two of them to start something up. Perhaps the deadline of 108 chapters was closing in too fast, leaving no time...?
Toy Ship: NanaxMayu to some fans, despite there being no hints of this in the main series.
The Diclonii. The viewers are supposed to sympathize with them but it's easier said than done. Whatever Diclonii we see that's not in the Facility is going around randomly butchering people, and then there's the implications that they're genetically predisposed to wiping out the human race, which can make the intention of sympathizing with them develop the opposite result.
Lucy is played up as a Tragic Villain, but some find it hard to feel sorry for her when she murdered Kouta's family out of petty jealousy and was Easily Forgiven for it in the anime. It was also shown that before she met Kouta, she killed families just so she could stay at their houses at night. You could count with with your fingers how many people she killed that actually deserved it.
We're supposed to see Nozomis dad as a Well-Intentioned Extremist because he's willing to do anything to prevent Nozomi from getting the same voice defect her mother got (which caused her to commit suicide) by resorting to physically abusing her. However the fact that there were clearly other ways of protecting Nozomi (such as warning her about the voice defect, for Pete's sake!) only makes what he did very inexcusable to say the least, as well as making him come off as a cruel asshole rather than a protective father. It doesn't help either that it almost looks like he's grinning sadistically while abusing Nozomi.
Values Dissonance: A major reason why the manga wasn't released in English for well over a decade was because the series is too hardcore even for American audiences. The anime may be extreme, but the manga may be even worse, and no U.S. licensing company wanted anything to do with a series that involves brutal murder, torture, rape, and with children being victimized, lest they face controversy from all angles. It took 17 years for Dark Horse Comics to finally step up and license the series, which most likely owes itself to the sheer internet following Elfen Lied has attained after all this time.
Wangst: Yuka being angry at Kouta for not remembering their childhood even though it's due to the trauma of seeing his father and sister being slaughtered in front of him (and it's implied that she knows Kanae didn't die from an illness, so it's likely that she knew about their fate) probably has something to do with the fanbase's dislike of her. Not helping matters is that the anime tended to exaggerate this beyond what it originally was in the manga (example: in the manga, Yuka did not want Kouta to grope her breasts and was prepared to sock him if he tried, with the moment being Played for Laughs, but in the anime she seriously did want Kouta to grope her breasts in order to show her the same "affection" he'd been showing Nyu, whom Yuka had grown jealous of, and runs off crying and declaring her hatred of Kouta when he refuses her request.)
Anime only. Bando does some stupid things from attacking his own partner, getting up to Nana's range despite knowing better and trying to jump for his gun once Nana has knocked it away despite already having another one. (In the manga he barely had time to reach for it before Nana stopped him)
This is a far cry from his manga counterpart who always played it smart. Even during his first battle with Lucy after she had taken him down he attempted to find a way to beat her...even if such a thing didn't work out in the end.