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.
Is Jobe Wilkins well meaning if Jerk AssMad 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?
Jade as written by Babs Yerunkle is a mature young woman struggling to overcome physical limitations and the dangers presented by the world with the help of her friends. Jade as written by Diane Castle is a Crazy AwesomePsychopathic Girlchild who is a continual source of crazy, entertaining things. YMMV on which version is better.
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 Invulnerable cyborg 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 (namely, 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.
Fetish Fuel Station Attendant: ...Sara, a half (or 3/4, depending on your math) demon. Her father was a demon of lust. She has tentacles, shapeshifting abilities, a will to use them, and she's OmniSexual. At one point, to taunt someone she sticks out her tongue, which grows to three feet long, and sprouts tendril-like fingers.
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. X)
Personality-wise, it often varies between authors. Whether and to what degree someone is sadistic (but never caught), competent (when no one else is), powerful (at the expense of plot) or annoying (yet no one in story catches on) changes depending on who's in the spotlight.
Phase turned her into a monster by trashing her BIT (accidentally), and keeps thinking about it despite the fact that he never intended to do it and despite the number of Exemplars he did the same thing to, none of them got their BI Ts trashed.
He likes Brass Monkey (an alternative band) that the majority of other characters hate. They never stop bitching at him about it.
When he was a child, he donated millions of dollars to the MCO and supported Emil Hammond, believing that the doctor was a good guy who was being slandered by a lot of people with a grudge. Ayla found out the truth, and now he won't stop beating himself up for it- despite repeatedly being told by his friends that nobody would blame a kid for donating money to a cause that his parents told him was right.
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 Transgendered 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 trans-gender 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?
Tear Jerker: Phase discovers that Fey's spells have been drawing Essence from nearby ecosystems, killing many of them. Fey is horrified and realises that she may have caused horrific amounts of environmental damage.
Nacht meets her mother, who orders her around like a servant, demanding loyalty despite doing nothing to earn it. She mocks Kate for asking about her unknown father, and forces her to secure a magical object to learn more about him. At the end of their conversation, Nacht hugs her mother, and her mother asks why. Kate just says 'Just finding out what it was like.' It's safe to say that the Bell Witch is a huge bitch.
The "glamor" mutants like Medusa, Fey or Sara have essentially makes them extremely attractive to people or causes sexual arousal in people affected by it, to the point that some of these powers can bypass even sexual orientation — See Even the Guys Want Him above. Whether or not this is a form of mild Mind Rape (or actual rape, if they do anything with it) is up to the reader.
The biggest one might be the fact that all the LGBT students are segregated from the rest of the school and asked to remain in the closet. The school attempts to justify this by saying that anti-queer bias is so deeply ingrained into Western society that homophobic bullying would be inevitable and apocalyptic in proportion, and all it would take is one incredibly angry homophobe for a tragedy.
And the most unfortunate part of that implication: The semi-official cover story for that dorm, obliquely hinted at by the school administration whenever someone outside the dorm wonders why so many Poesies seem a little "off", is that it's the dorm for students with mental problems.
Fridge Logic makes it worse: In canon people have an easier time accepting the fact that people at the school are very much non human than they do that that the hot chick might've been a boy until recently. If for example, Poes was instead "Every Jew, Muslim, Hindu, and Buddhist must hide their faith here because the world is simply too intolerant" it would never have gotten off the ground, which in and of itself just shows the blatant fetishism of transgendered people inherent with the series.
Funnily enough, in Real Life bashing LGBT people has become distinctly something that is not tolerated by Western society more and more, making the justification even more unfortunate.
Keep in mind that 1, the person who instituted the cover-up is in her seventies and did so decades ago when such attitudes were more respectable. 2, people aren't asked to remain in the closet, they are free to come out (individually; no outing of the cottage as a whole). 3, Poe's purpose is to give the LGBT students a place to be themselves without fear of oppression (well, OK, excepting people like Sharisha and Hippolyta, but thankfully they're the minority), and 4, if Poe was known as the cottage for LGBT people, everyone in there would be outed. At least with the cover-up, they can decide whether or not they want to be out, as opposed to having that choice taken away from them. 5, all of the cottages are populated by specific groups- Whitman and Twain by GSD students, Emerson and Dickinson by non-GSD students, Melville by students of high-profile (i.e. Alphas, a lot of Bad Seeds and Capes), Hawthorne by students with issues controlling their powers- everyone in Poe is clearly there for a reason, so how many explanations are there for why those specific students were there.
After being a girl for only six weeks, Tennyo defended herself against a sasquatch-like mutant who had been trying to bully her by flipping him over her shoulder and pinning him to the ground after he grabbed her. When a teacher heard rumors about this event, he chastised her for not acting enough like a girl, implying that girls should act according to outdated stereotypes and that standing up for yourself, even if you are able to, is improper for a girl.
The fact that the sole FTM of Team Kimba is the only one without his own set of stories.
The Meta-Unfortunate Implications inherent with people speculating that he is actually a villain because of that, and not that FT Ms are basically ignored.
Second Law of Gender Bending takes place incredibly fast, even from characters virulently hating their situation. Fey for instance spends all of about a day worrying that she's become fully female, before giggling and deciding to take Tennyo on a shopping spree.
The Goodkinds is just a landmine of unfortunate stereotypes surrounding conservatives; perhaps not undeserved but still. What's worse is that despite their flagrant human rights violations (as in constantly) they manage to control the country to an extent and the superpowered community are powerless to stop them.
The Third Law of Gender Bending tends to permeate most of the stories. By the time they arrive at Whateley, the four main characters who are shifting from male to female have all acquired the habits of tittering endlessly, pillow-fighting, constantly talking about their periods, and blaming everything on their hormones because that's what women do.
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.
What The Hell, Teacher?: The "Gun Safety" Instructor is apparently such a paranoid psychopath that he physically assaults students for the "crime" of creating an illusion of a firearm. As a demonstration of what their illusions are.
And he deactivates the safeties of a Danger Room, assigning it to try to kill Loophole, so that her mutation will activate against her will. What if the mutation was mind-reading or supersenses? What if her mutation was an extreme GSD?
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.