Is Jobe Wilkins evil, or a well-meaning if JerkassMad Scientist who genuinely can't understand that his attempts to help are worse than the original problem? On the forums even the canon authors have disagreed on this point, but the author of the Book Of Jobe goes for the second viewpoint.
Team Kimba: Powerful, but made up of compassionate and heroic individuals, or an Affably Evil subversion of True Companions whose members have almost no sense of restraint or mercy, care more about each other then the rest of the world, and are each a danger to the rest of humanity foronereasonoranother?
Angst? What Angst?: Particularly in the early stories, where the relatively frequent deaths of students, faculty or staff doesn't seem to bother anybody much. Rectified by later stories revealing that some characters are actually suffering a lot, just not always in ways apparent to others.
Try asking the fanbase whether they think Englund should have expected the Syndicate to go back on their deal and invade the school. Half of them think that he couldn't have possibly seen it coming, and the other half think he should be crucified for letting them into the school.
Deathlist is a psychopathic, Nigh Invulnerablecyborg who gets off on widespread carnage and considers the world to owe him a debt of pain. The most horrific thing he's done so far was to kidnap a mutant superheroine, jam a power-neutralizing device into her skull, then hack off her arms and legs and give her to his troops as a sex toy. Then, when she died after more than a month of torture and rape, he impaled her corpse on a pole with a thank-you message to one of her former teammates carved into her chest. Not even his Freudian Excuse—that his parents tried to kill him by crushing him in a garbage compactor—nets him any sympathy after that.
Hekate is a wizardess supervillain-in-training whose rap sheet includes using a spell to enslave two of her classmates for a year, during which they were repeatedly raped and otherwise abused while being completely aware of what was happening but powerless to stop it, as well as the fact that the athamé she used in the spell was empowered by the ritual sacrifice of two young children. Not only that, but during a magical battle with Fey, after trying and failing to ensnare her in the same enslavement spell mentioned earlier, she summons a trio of iron elementals using the promise of dozens of future sacrifices. To top all that off, she used her athamé to stab Jade in the heart beforehand, just to torment Fey.
For example, imagine if the neighborhood daredevil developed a healing factor. What does he do? Go into business as a paid guinea pig/test pilot for the mad scientist students' more iffy experiments at the school.
And he lets Phase rip off his dick in the cafeteria. At lunch. In front of the entire school.
Jade Sinclair, 'Radioactive Condor Girl!' In fact, this is Diane Castle's goal in writing her.
Designated Hero: Almost every main character has had moments of these, but special mention goes to Sara — who rapes (in both ways) the resident JerkassMad Scientist because she thought it'd be useful to have him angry at her, and Chou, who goes around killing people because a magic sentient sword told her to.
Designated Villain: The Goodkinds shift between this and Knight Templar. Possibly lampshaded, since Ayla is quick to defend his family, AND retains contact with a few.
Ensemble Dark Horse: Amongst people who dislike the series, Ayla and Jade are more popular for having more balanced powers and a more respectful take on transgender issues.
Hollywood Homely: When everyone else is an exemplar, minimum, the characters who are baseline in appearance (or worse) are pretty screwed. Or not, actually... Ayla comments a lot on this. (Actually, only about a third of the characters are Exemplars, but it does make a difference.)
Love to Hate: Jobe Wilkins. He's an obnoxious and grating Jerkass and acknowledged as such in-universe. But reading about him, you can't but laugh at his egotism and his blatant lack of respect for other people. It helps that we have characters like Jadis around to make snarky remarks at his expense.
"Sara's Little Purple Book," a guide to mutant sexuality, varies between Funny and this.
Two words: Dark Generator. In the sim, her first attack (apart from Shroud going rogue too) is to animate part of Melville Cottage, turn it into a 30-ft golem and send it to attack. That is, not only part of the building, but everything in it, including furniture, possessions and people.
Elaine Fleischer collaborated with the police to capture a rogue devisor who turned all his male subjects into beautiful busty women who were all slavishly devoted to him. While Delta made it out as a fully-functional girl and the guy got caught, his minions want her dead, and Phase at one point speculates that Delta actually did get the mind control treatment and just doesn't know it.
All of the story Tennyo Goes To Hell, especially the second part. We find out what happened to the people Sara ate, and it's not pretty.
Cavalier and Skybolt. After Fey and Jade rescued them, they were sent to ARC for treatment and therapy. And it hasn't worked. They've done pretty much nothing but sit together and barely react to anything, the notable exception being trying to separate them.
Macrobiotic's family has been constantly waging war against a super villain called Deathmaiden, who keeps returning no matter what they do. Deathmaiden blew up Macrobiotic's father, and will most likely go after Macrobiotic and her mother when she next returns- which, as Macrobiotic notes in Ayla And The Mad Scientist, is a mere couple of years away.
Squick: Several examples. Almost all the main characters are transgender in some way shape or form and there are rather frank discussions of gender issues in the early chapters — for example, Ayla is mostly female except for... certain elements of his body, Jade uses her powers to "tuck" herself in and this is described rather frankly — did we mention that Jade is physically 12 years old? Sara essentially vomits out her entire set of internal organs when she "awakens". For the most part however, the series is a fairly standard slice-of-life high-school drama, except with super-powers. If you're squicked by transgender stuff, why are you reading Whateley stories?
Jobe's design for an organic prosthetic penis, which was essentially a parasitic worm that attached to the vulva. What objections could women possibly have to that?
Values Dissonance: Multiple examples, mostly as a result of the odd balancing act a super-neutral school would have in dealing with super-heroes and super-villains.
Merry could also qualify, the chewtoy that she is.
As above, Greasy shifts to this when Peeper's abuse is taken seriously.
'Ayla and the Mad Scientist' has Fey finding out that many of her big fights have resulted in the destruction of entire ecosystems because she was drawing more Essence than they could give her. She accidentally killed entire forests.
In 'Ayla and the Great Shoulder Angel Conspiracy, Part 5/6', Billie's memories of being the Star Stalker are unlocked. As a result, she remembers the millions of people the Star Stalker killed, and because she's got it stuck in her, she ends up believing that she, Billie, killed them.
She had a thing with Harry Wolfe which ended badly when Hexette stole him. Not only is Tennyo still wondering about her sexuality, she lost her chance with the only person she's romantically interested in.
She's incredibly shy and doesn't have many friends, mainly because nobody wants to be her friend.
Chou's father is stuck in the personal clutches of a demon with a grudge.
Josie Gillman, a designated Butt-Monkey and comic relief character, is actually an aversion despite the universe constantly conspiring to humiliate her. Her Pollyanna, Cloudcuckoolander and Wrong Genre Savvy tendencies prevent her from seeing anything, no matter how humiliating, as more than a temporary setback.