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.
YMMV: Book of the New Sun
Designated Hero: Severian is often very unlikeable, and his actions are rarely, if ever, heroic.
Epileptic Trees: Whole groves of them. Some people have claimed that Dorcas might actually be a vampire.
Les Yay - Severian speculates that this happened between Dorcas and Jolenta during his absence.
Moral Event Horizon - Severian's rape of Jolenta. Of course, he's spent most of his life torturing people, so he might well have crossed it years ago, dependent on the reader.
Of course, It is highly questionable whether it was non-consensual or not— it might have been Severian's guilt about the rough nature of the sex — and she didn't really resist. Like the rest of the book, it's hard to know.
Nightmare Fuel: Jolenta's eventual fate. Originally a homely woman, Dr Talos made her very, very beautiful. So beautiful that Even the Girls Want Her. It's left vague exactly how he did this, but strongly implied to be the reason why she's so weak and lethargic all the time. Then he and Baldanders leave, and the treatment starts to break down, and Severian feels metal bands under her skin holding her body in shape.
Rewatch Bonus: There are many hidden aspects of the story. Including:
Dorcas, Severian's second true love, is also his grandmother.
The tomb Severian spends much of his free time in as a child is his own. Hilarious in Hindsight because in one of the early chapters of the first book, Severian specifically notes that the funeral bronze on display in the tomb has similar facial features to his own.
For some, the appeal of the Urth cycle lies in trying to uncover the 'true story', to which the events of the plot, seen through Severian's extremely subjective gaze, allude.