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: Aurang and Aurax are the twin princes of the alien race, the Inchoroi. After crash-landing during the height of the mystical Cunuroi civilization, a war broke out between the species. Aurang and Aurax were the only survivors of the Inchoroi and engineered a plague that killed every female member of the Cunuroi and made the males immortal so they'd suffer forever. They also helped create the Sranc, hideous creatures whose existence is simply pain and lust so that the only way they interact with other beings are killing and raping them. To prevent their own damnation for their sins, the two plan to fill Hell with so many souls, the door will be shut permanently. For this end, Aurang and Aurax mastermind hundreds of horrible murders, engineer genocidal wars for their own ends, and created a being called the No-God that killed every baby to be born for a decade. Aurang and Aurax are also sexual sadists who are fond of rape as an interrogation method. Aurax in particular enjoys raping a victim's wife in front of him before giving her and said victim's family to the Sranc long after it is clear none of them have the answers Aurax wants.
Epileptic Trees: Fan theories on the nature of the No-God can sometimes veer towards this, as well as many about Kellhus.
Ho Yay / Straight Gay: Moenghus and Cnaiur, which resulted in Cnaiur killing his father. This is the reason why there is latent Ho Yay between the adult Cnaiur and Kellhus, even though it's more like Foe Yay.
YMMV. I didn't read it as much as Ho Yay as Moenghus playing an evil mentor and persuading Cnaiur to kill his father and seize control of his tribe, in the name of some vaguely ubermenschish philosophy of "Forsake tradition, do what you will"..
They're explicitly referred to as lovers and there's plenty of kissing and touching while Moenghus is dying, so "seduced" is not metaphorical there. Considering Serwe and Anissi, Cnaiur's more Bi the Way.
Magnificent Bastard: Kellhus. He is biologically human, but mentally and ethically an alien without emotion. To assume control of the Holy War and make entire nations follow him, he decides to do it through religion. Kellhus slowly transforms their entire religion with himself as the Jesus Christ figure.
Marty Stu: A deliberate lampshaded example for Anasurimbor, since he has most of his father's inhuman abilities while also being capable of love.
Seswatha's memories of the Apocalypse are literallyNightmare Fuel. The Mandate sorcerers dream it every night so they can never forget what it is they fight against. For example, Achamian once dreams of the fall of the city Sauglish. Grown men are dashing their babies' skulls against the street so the Sranc can't rape them to death and then rape the corpses. The Apocalypse is thirty-two years of Tear Jerker: Achamian virtually never refers to it without calling it "heartbreaking." Oh, and the No-God? His very existence is such that babies can't be born alive if he is. The eleven years of the No-God's existence were called "the Years of the Crib" because all babies were stillborn.
The epilogue of the second book, where the Inchoroi appear onstage, is the single most horrendous scene in this whole series, and that says a lot.
The experiments of the Dunyain upon human captives. To learn how to manipulate people by reading their facial expressions, their young are taught "neuropuncture". In this process, living captives are strapped down and their faces dissected, so teenagers can experiment with their facial muscles. While they're still conscious.
The black halls of Cil-Aujas.
The view of damnation in the afterlife that we get from Mimara's Judging Eye in The White Luck Warrior.
Shaeönanra's backstory. Also, his present physical form.
Squick: The Inchoroi are a self-described "race of lovers", wholly obsessed with sexuality, sexual violence, and rape of all sorts. And it only gets worse from there on. As a reviewer aptly put it: "Scott Bakker's books are not dark and gritty. They're pitch-black and sticky."
Some Anvils Need to Be Dropped: Kellhus corresponds to Jesus Christ. To unite mankind against the Consult, he takes control over the Holy War by intentionally reforming their religion, making them view him as a Messiah. Kellhus is tried as a heretic, hung up and left to die and then returns to life to ostensibly save everyone's souls. Oh, and he takes as his symbol the "Circumfix", which is the thing he was hung to die on.
And yet no-one knows if he's good or evil.
He's closer to an Anti-Christ . . . but this is set in a universe where such a being is probably necessary if humanity is to survive a potential Second Apocalypse.
Bakker's point in general - that people are ignorant of the cognitive biases and mental errors that condition their thoughts, and ignorant of their ignorance - might qualify as one.
Squick: These books are not for easily disturbed readers.
Incest between Emperor Xerius and his mother — especially when she gets a teenage sex slave for him, and Xerius makes his mom stay and teach the girl how to "properly pleasure" him.
A scene where the Mother-Supreme of Yatwer's cult smears blood from her period in the faces of male worshipers, "a red line of hatred", after having sex with them.
Tear Jerker: Many examples. This is probably the most depressing well-known fantasy series.
Achamian is tortured by the Scarlet Spires. His best friend Xinemus, a religious man who is conflicted about his friendship with a "blasphemer", comes to the rescue. But the Scarlet Spires subdue him and torture him as well along with Achamian, gouging out his eyes. When Achamian escapes and finally returns to the war camp, Esmenet (the woman he loves) has left him for Kellhus. The saddest part was that she had sold herself into sexual slavery to return to Achamian in the first place.
The scene where the little orphan boys watch Maithanet's procession through the streets. It's depressing because one of them prostitutes himself because he's too scared to steal, and because orphans are not considered "real children". The scene ends with that boy being taken away by a slave trader.
Cleric and his fate. Achamian was forced to kill him, because Cleric (who was insane from amnesia) loved him and Mimara to the point where he tried to kill them, in order to remember them.
Kellhus' Great Ordeal starts running into this. The Ketyai of the South, seventy thousand strong and led by King Umrapathur II of Nilnamesh, are totally annihilated by the Sranc Horde and by attacking Bashrag, while the Grandmaster of the Vokalati goes insane and starts killing both soldiers and Sranc with his sorcery. The Grandmaster of the Mandate then has to kill him, causing a battle between the Mandati and the Vokalati even while tens of thousands of soldiers are being raped to death by the Sranc below. Umrapathur dies praying that the Great Ordeal will survive him, even as the Sranc begin violating him. When Kellhus finally arrives to rescue them, the sorcerers have survived but only "scant hundreds" of the soldiers on the ground still live. Holy shit.
Uncanny Valley: Like all Nonmen, he is tall and superhumanly beautiful, with marble-white skin. But there's something very "off" about him, which all characters note. His teeth are fused, his face has the same features as a Sranc, and his voice has the "tones of a deformed child woven into it."
Unfortunate Implications: Bakker's four most prominent female characters include two whores (although one of them becomes Empress of the Three Seas, and the other is no longer a whore), a concubine/sex-slave, and a sexually predatory queen. This has led to a great deal of debate among his fans (and many who aren't) over whether this represents misogynist intent on his part.
The man himself says he/s going for mould breaking/realism: "The tendency in much fantasy fiction is to cater to readers’ moral expectations, to depict ideologically correct worlds and so avoid all the kinds of trouble I seem to get into with my fiction. In other words, the tendency is to be apologetic rather than critical (and then to be critical of those who refuse to apologize). My interest lies in the glorious ugliness that is a fact of traditional world making. Bigoted worlds. Biased worlds. Human worlds expressed through fantastic idioms."