Cadence was very well-received despite her small-but-pivotal role in the first book, which meant everyone was very happy when she became a main character in the second. She's mostly liked for her sass (mixed with Pet the Dog moments towards Morrigan), and the fact that her powers are seriously cool.
Israfel only has two scenes in the second book, but those scenes are pivotal, and he leaves quite the impression. There's also a vocal set of fans who like to ship him with Jupiter, increasing his popularity.
A lot of the fandom really likes Morrigan's grandmother, for being her only relative that actually seems to give a crap about her, and her take-no-shit attitude.
Roshni is a minor character who gets a lot of love, partially because of her job at the very awesome Gobleian Library, but mostly because she's Miss Cheery's girlfriend.
Evil Is Cool: Ezra Squall is a murderous bastard, but he's a murderous bastard with style, and who wouldn't want powers like his? His coolness also makes the scenes where Morrigan stands up to him even more impressive.
It's commonly agreed that Jupiter is gay or otherwise queer.
Noting the similarities between the descriptions of Noelle's singing voice and Israfel's, it's nigh-universally agreed that there is some sort of connection between Noelle's knack and the Celestial Beings. Popular ideas include Noelle being half- or quarter-angel, or her parents having bought her knack off the Ghastly Market.
Harsher in Hindsight: Word of God actually invoked this on her Twitter. She plotted and wrote Hollowpox well before the Coronavirus Disease 2019 Pandemic, but the pandemic was in full swing before the book became available to read, leading her to note in this thread that she unintentionally predicted a lot of what would happen.
Jessica Townsend: Anyway, look out for the bit in Hollowpox where an incompetent politician puts out warning posters all over Nevermoor with the vague, unhelpful advice to STAY ALERT.
(Unless my editor makes me take it out, which... suddenly seems likely.)
He's Just Hiding: The last time we see Mildmay, he's running from Squall and his army, with Squall clearly intent on killing him. Mildmay isn't nearly as powerful or competent as Squall, and Squall isn't the sort to leave any loose ends, but because we never see a body or get outright confirmation of his death, some fans speculate he might've escaped somehow.
Cadence has an obvious soft spot for Morrigan, and is far nicer to her than she is to anybody else, leading to scenarios where it seems like she has a crush—such as "borrowing" a stranger's dog to bring to Morrigan on her birthday because she thought she would like it, and being the only member of Unit 919 besides Hawthorne who doesn't hesitate to do what she has to do to protect Morrigan from the blackmailer with no complaining at all.
Nurse Tim describes Jupiter as a "a bit of a flirt" in a way that implies he knows because Jupiter was flirting with him.
Iron Woobie: Morrigan Crow in a nutshell. She has been through so much, and yet manages to remain a kind, curious young girl who keeps going in spite of her fear.
It Was His Sled: Ezra Squall is the Big Bad, and Morrigan is a Wundersmith. It's virtually impossible to discuss the series without mentioning those two facts, even though they're huge twists in the first book. The second one is especially hard for new readers to avoid, since the second book is literally called Wundersmith: The Calling of Morrigan Crow.
Cadence isn't the nicest person, but there's no denying that having powers that make nearly everyone forget about you or ignore you would be seriously rough. She softens up a bit towards Morrigan (and later Hawthorne), which also helps.
Alfie is a bully, but he still didn't deserve to be betrayed by one of his teachers, kidnapped, and have his knack stolen from him. Similarly, his girlfriend Heloise is a nasty little brat, but even Morrigan can't help but empathize with her pain over what's happened to Alfie.
Jerks Are Worse Than Villains: Most of the fandom dislikes Corvus (Morrigan's unloving father), Baz Charlton (an insensitive boor and overall pain), and Inspector Flintlock (a bigoted cop), way more than the series' actual villain, Ezra Squall. Part of this is Evil Is Cool, and the fact that Squall has shown some Hidden Depths that the other three mostly lack, and part of it is for similar reasons to why Dolores Umbridge is more hated than Lord Voldemort. Squall is a monster from your nightmares, the other three are assholes you have to deal with every day. (The fandom's hatred of Corvus, in particular, really cannot be overstated; some have joked that Squall at least encourages Morrigan and takes an interest in her education, which is more than Corvus can say.)
LGBT Fanbase: The series has picked up a definite following of queer readers, with LGBTQ+ headcanons for the characters being very popular, and many holding out hope for some canon queer characters in the series. Their wish was granted in the third book, which reveals Miss Cheery and Roshni are dating.
Memetic Psychopath: Ezra Squall's sociopathy and cruelty is played deadly seriously in canon, but the fandom will often play it for dark humor, usually with Morrigan as a Straight Man.
Periphery Demographic: The books have picked up an adult following, despite being aimed at middle school-aged children.
The Scrappy: Although he's not an out-and-out Hate Sink like Flintlock, you'll be very hard-pressed to find a reader who likes Corvus. Neglecting and disregarding the feelings of your young daughter is not a way to endear yourself to the fandom, Mr. Crow!
that she unintentionally predicted a lot of what would happen.Jessica Townsend: Anyway, look out for the bit in Hollowpox where an incompetent politician puts out warning posters all over Nevermoor with the vague, unhelpful advice to STAY ALERT.