Angst? What Angst?: Septimus seems pretty unconcerned about the disappearance of Nicko in Physik.
Anti-Climax Boss: The Ring Wizards. They have been built up as evil and dangerous, but their magic was thwarted by rocks blocking them from accessing the Alchemical Fyre that would have been used to destroy them. It gets worse when they are matched in power by a much younger Extraordinary Wizard (Marcia) and then quickly put back into their rings in no time at all by an even less experienced princess (albeit, this being her destiny). And all without the main character's help.
Awesome Art: Mark Zug's drawings of the characters and settings in the books.
Ending Fatigue: The books have an habit of lasting a long time, and even after the climax there is usually still a bit of plot before the end.
Fan-Preferred Couple: Septimus/Jenna and Marcia/Silas, in spite of the fact that Septimus and Jenna are adopted siblings, Jenna herself is given an apparent canon love interest in the form of Septimus's best friend Beetle, and that Silas is married and has seven kids (one of which is Septimus himself).
Harsher in Hindsight: The events leading up to the outbreak of the Darke Domaine in Darke bear an uncanny similarity to the Fukushima accident, namely the safety lapses in both cases.
Informed Wrongness: Jenna is a Barrier Maiden and is told to go away in Syren rather than get into danger, notwithstanding the fact that she isn't outside of the Castle.
Shipping. Many: Septimus/Jenna, Marcia/Milo, Marcia/Marcellus... the list goes on and on. Septimus/Syrah flopped, after being teased in Syren and Darke, gets a Thunderflash through the hull in the epilogue of Darke.
Slow-Paced Beginning: A few people complained about the length of Queste's introduction, specifically the Merrin Meredith scenes.
They Wasted a Perfectly Good Character: Arguably, Septimus Heap himself. He was the Magical Seventh Son with great magical potential that even Marcia said could wipe out the darkness. But after seven whole books, his powers barely developed at all. He was still in training when the climax of Fyre came and went, which was resolved by Jenna instead of him. Some might argue that all of his major character arcs were concluded by book six, so it didn't seem like there was much for him to do in the finale.
Complete Monster: Mitza Draddenmora Draa is a treacherous woman who has no concept of friendship and no genuine love for anyone. Envious of her stepsister Cassandra for marrying Dan Moon—despite no longer caring for the latter—Mitza murdered Cassi with an envelope full of Sand Flies, putting Cassi through a lengthy, fatal illness. Allying herself with Oraton-Marr, Mitza kidnaps Dan and leads a pack of Garmin to abduct nearly everyone in the PathFinder village so that Oraton-Marr can make them dive for a submerged Orm Egg, knowing that many of them would not be able to breathe underwater and would not survive the task; Mitza also tries to ensure that her 12-year-old niece Tod would be taken as well. Remaining with her allies as they escape with the egg, Mitza is willing to drown the Apothecary's baby to force the Apothecary to assist them and prevent interference. Mitza later plots to kill Tod with Sand Flies to spite Cassi's memory, at the same time aiding the Red Queen in invading the Castle in hopes that she would cause death and destruction, and nearly succeeding in poisoning her niece.
