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.
Complete Monster: Vicar Zhaspahr Clyntahn is Grand Inquisitor of a Corrupt Church, which tells you all you need to know. However in the fourth book, he not only executes every vicar in the Church who even thought about opposing him, but their families as well, including children as young as twelve. This act is monstrous enough that a declaration of Holy War that had been hanging over the plot since the second book is rendered an afterthought.
Magnificent Bastard: Subverted; Kahlvyn, Duke of Tirian shows every sign of being one, but is then killed off very quickly.
Moral Event Horizon: The Ferayd Massacre and (in the eyes of Church Loyalists) the Charisian response to it.
Clyntahn's treatment of anyone even remotely associated with the Wylsynns is this for Duchairn, who comes to view voting for the invasion of Charis as his own.
It takes a lot to turn a declaration of Holy War into an afterthought. Clyntahn pulls it off.
How Firm A Foundation also shows that this has become an In-Universe Moral Event Horizon, as it cements Clyntahn's status as a complete monster to anyone who isn't plain ignorant or as fanatical as Clyntahn himself.
Protection from Editors: The books are quite long and could use a little tightening. One example would be the jargon-laden, plodding opening chapter of How Firm A Foundation which is about a ship getting fighting to avoid running aground in a storm; it really contributes nothing to the plot, though it revisits two minor side characters and shows off Weber's knowledge of sailing.
The later books also show spelling errors, characters called by one name when the narrative clearly means another, occasional confusion between Charis, Chisholm, and Corisande and a changing in the name of Hektor Aplyn-Ahrmahk's duchy from Darcos to Darcos Sound.
The first five books contain the story that Weber had originally planned for book one. He's openly stated that he's deliberately dragging things out to put his kids through college.
Recycled Script: The overall premise of the series (Musket-era Feudal Future, Path of Inspiration repressing technology, etc.) was previously used as one major plot-thread of the third book of Empire from the Ashes, and the concept of a race of genocidal aliens intent on wiping out all other sentient life was first used in the series as a whole.
Shades of this same concept are seen in the war between Grayson and Masada (Space Amish religious fanatics whose war went nuclear). Humanity's Space Navy, seen briefly in the Safehold series, strongly resembles the navies of Honor Harrington. The tossed salad genetics and wildly diverse names were also seen in Honor's world. Indeed, it seems almost every idea hatched in the Safehold universe was incubated in one of his other series. Not that that's a bad thing.
War Ship: Cayleb & Sharleyan, given they started out as (albeit reluctant) enemies.