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.
Alternative Character Interpretation: Is Jesse Custer broadly in the right for most of the series, but with a few flaws, or is he initially a macho, judgmental asshole who learns to be more forgiving and empathetic over the course of the run?
Within the series, you have Jody and TC, who are Complete Monsters (as seen below) in the main book but get an upgrade to Heroic Comedic Sociopath in their one-shot.
Marie L'Angell is the terrifying grandmother of protagonist Jesse Custer. She takes "controlling" to a new level and views her own family as tools rather than people. Her usual punishment of her grandson Jesse was locking him into an airtight coffin with an air hose and letting him wallow in his own shit and piss for a week. Then, she attempted to kill her daughter Christina for trying to stop it. But the worst of Marie's cruelties is her obsession with "hardening" Jesse by destroying all his non-family ties, including his puppy dog, his girlfriend, and his childhood friend. And his own father.
Jody is generally the instrument of this. Unlike Marie, however, Jody makes no pretense that he doesn't enjoy what he does. We see what a total scumbag he is when he blows Jesse's father's brains out right in front of him and then sneers "fucking crybaby" at a tearful Jesse. When Jesse's dog tries to be friendly to Jody, Jody nails its head to a post and then brutally beats Jesse into submission for it. Years later, Jody forces Jesse to cry 'uncle' while twisting his arm so bad the bone snaps out. In the present times, Jody pulls a repeat again when he shoots Tulip in the head at Marie's request. While Jesse watches. With that smug, superior expression all the while. Later, when Marie finally orders Jesse's death, Jody isn't content with just killing him, oh no. He has to break and humiliate him and make him beg first. When Jesse finally strangles Jody to death, Jody is too twisted to feel anything but pride that his abuses turned Jesse into a killer.
Crosses the Line Twice: More like it crosses the line six times and is still looking for the next line to cross, with no sign of stopping.
Though part of her rant — "Nobody coddled you and wiped your asses for you! Your lives didn't turn out the way you wanted them to?>" — comes off as extremely misguided given that he's an abused kid and a bullying victim who can't even move out despite being eighteen because his father is the sheriff (and the person delivering the "You Suck" speech herself implicitly did nothing to help him out earlier when she found all of this out). The whole thing comes off as a Kick the Dog and misplaced anger on the sister's part as much as anything (especially since the entire suicide plot was her brother's idea, not Arseface's). Notice that his life doesn't really improve much until Jesse shows up and inadvertently drives Arseface's father to suicide.
God-Mode Sue / Villain Sue (Until his quasi Heel-Face Turn): The Saint. Nothing can kill him and he can kill everything. At least Jessie getting him once with the Word of God showed he wasn't completely invincible.
Harsher in Hindsight: Cassidy's loving tribute to New York City is capped by a city skyline focusing on the World Trade Center, which would be destroyed only a few years after publishing.
In-Universe, Jesse comes to reevaluate many of his past adventures with Cassidy this way late int he series after he learns about Cass's history of succumbing to his weaknesses and dragging others down with him.
HSQ: Just keeps going up and up in the War of the Sun arc. The Saint goes from kicking a tank to being hit with a nuke!
Idiot Plot: The Salvation arc. Jesse could take down Quincannon in a second with the Word of God. If he isn't going to, then Quincannon could have Jesse convicted and jailed just as easily. The arc is only made possible by each of them making it a matter of principle to settle things "personally" instead of being practical about it.
Magnificent Bastard: Herr Starr. Even after being nigh-completely mentally and physically destroyed, he's still just about the baddest motherfucker in the valley. (Okay. Second baddest.)
Arguably Cassidy int he final arc, given that he arranges things so that he gets to walk away with exactly what he wants while Jesse and Tulip think he's dead and won't come looking for him again.
Arseface - his father is an abusive Jerk Ass and most of his peers aren't much better. Then he is horribly disfigured by a botched suicide attempt and it goes downhill from there...
Sally, the homeless woman Jesse encounters who tells him Cassidy's history.
Starr is a villainous example. He Used to Be a Sweet Kid, then a pack of bullies decided to blind him/gouge out his eye by cutting a star into his face, something that also (somehow) left him bald. Then, in the course of the series, he gets raped by a Depraved Homosexual, finds himself unable to be sexually aroused by women anymore and has to resort to being anally penetrated by whores wearing strap-on dildos to get pleasure, gets a scar cut across the top of his head that makes him look like a giant walking penis, gets his genitals bitten off by a dog...
His poor assistant, Hoover, was just a shy, decent man who was working for the wrong people.