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.
Man who loves his children who is reluctantly forced to leave them to serve a higher cause, or schemer who uses and manipulates his children to further his ambitions?
Lillith Grimm: Abusive teacher who should be fired immediately? or Good Is Not Nice?
Also her relationship with Alexandra. Does she not really like her at all, protecting her only because she's a Replacement Goldfish for her sister? Or does she genuinely love her, and projects a cold facade because she's either emotionally damaged herself and doesn't know how to open up, doesn't want to interfere with her relationship with Claudia, or is afraid she'll be forced to expel her if she shows too much open liking for her?
Crowning Moment of Heartwarming: The dedication on a book given to Alexandra by the author, a ghost: "For Maximilian and those who remember him. Death only wins when you have been forgotten."
Darkness-Induced Audience Apathy: One of the reasons that Thorn Circle is the least popular book in the series. Pre- Character Development Alex is essentially a Chaotic Stupid brat with few qualms about lying or manipulating others and no capacity to consider the consequences of her actions. She is opposed by Dean Grimm, who in the first book is a Sadist Teacher who just barely loses out to Dolores Umbridge in terms of overall sociopathy, literally torturing her students physically and emotionally, up to and including beating Alex with a Staff of Striking, threatening to have her friends whipped, and threatening to obliviate her family so that they lose all memory of her. She shows barely a hint of remorse through all of this and it is quite clear both that she enjoys emotionally breaking Alex and that she is only slightly less evil towards other students. Meanwhile Charmbridge is a Crap Saccharine World that seems to embody all of the worst aspects of American private school system, and the major theme of the book (aside from the murder mystery) is the myriad ways in which institutionalized inequality and widespread bigotry conspire to make life at school a living hell for Alex and her friends. All of this is very well-written and even believable, but many first-time readers fully expect the story to end with a Murder-Suicide by half-way through the first book.
Honey the Foul-Mouthed Ferret and Charlie the Smartass Raven are quite popular as well.
Foe Yay Shipping: Larry/Alexandra is one of the more consistently popular pairing in the author's shipping polls, though it's usually second to Alex/Anna and since the Stars Above it has been relegated to third place after Alex/Brian.
Fridge Horror: The Deathly Regiment are the souls of children who were sacrificed as part of a deal between the Confederacy and the Generous Ones. Thing is, the Generous Ones never asked for children to be sacrificed to them. The Confederacy offered. Given that the Generous Ones had no problem with Darla and Innocence being sacrifices, they evidently don't care who gets sacrificed, even if (as in Darla's case), the sacrifice is too old to qualify under the old rules (which said that the sacrifice must be too young to wield a wand).
Genius Bonus: People with sufficient knowledge of classical mythology were able to deduce the existence of a third Grimm sister early in book 2 from the revelation of Diana Grimm's middle name.
Growing the Beard: The first book mirrors the plot of Harry Potter and the Philosopher's Stone fairly closely and in many places seems more like a deconstructive retread than a story of it's own. The second book is where many of the more interesting and morally ambiguous characters are introduced or come into their own (Darla, Diana Grimm, Maximillian, Abraham Thorn) and the series develops a mythology and overarching plot of it's own while introducing many of the story elements that separate Alexandra Quick from Harry Potter (e.g. Dueling, Magical Experimentation, Long quest sequences away from school).
Iron Woobie: Tomo Matsuzaka. She's the only one from her culture at the school and is being abused and viciously bullied by much older students out of racism, but her only response is to stick it out and fight back.
The Alex/Anna ship also consistently wins the shipping polls.
Moral Event Horizon: The Confederation is a bunch of JerkassSmug Snakes from the very beginning, but when it's revealed that they sacrifice a child every 7 years in order to stay in power, they permanently establish themselves as the series' villains.
There is a substantial minority of readers who think that Lilith Grimm's behavior in book 1 permanently disqualifies her from ever being sympathetic.
Many viewers felt that Abraham Thorn crossed the line when he crashed a muggle train and caused the deaths of dozens of innocent people.
It's easy to sympathise with Darla wanting to prevent the death of her sister, but when she shows that she's willing to kill a child and her own familliar to achieve this end, she goes right of the slippery slope.
Heavy YMMV on this one. Most readers still consider Darla a sympathetic character.
Elias Hucksteen's personal horizon came when it was revealed that he ordered a teenage Claudia Quick to be forcibly sterilized.