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.
Marquis' involvement with Iron Rain, and Jack Slash's assertion that he did not kill her, have lead some readers to speculate that he did not kill Iron Rain, but blamed himself for her death. (Interestingly, Panacea's mother has never been named. Some speculate that Iron Rain was Panacea's mother, and that Marquis blamed himself for her death, possibly at Allfather's behest.)
Really, the story is filled with this. A common comment on Wildbow's writing is that he rarely ascribes purely negative or purely positive qualities to his characters, making their moral position whatever the reader ascribes to them.
Base Breaker: Saint. Any mention of him in the comments is likely to start a long and sometimes heated argument about whether what he did to Dragon was justified.
The protagonist Taylor as well. While some would argue her actions were justified, not everyone can agree on the more terrible ones.
Broken Base: Taylor's actions in the penultimate chapter. Did they count as bullying or not? If so, were they justified given the threat humanity faced? (And the billions said threat had already slaughtered?) Has Taylor fully transitioned into a monster like those who tormented her, or were her actions a necessary evil against a threat that could be stopped no other way?
Complete Monster: Jack Slash, full stop. The man's spent his life murdering his way across the country, and his personal bodycount has to be in the hundreds at least. That's not to mention everything he leads the Slaughterhouse Nine in doing, like attacking a hospital and targeting the maternity ward first. He eventually embraces his role as the catalyst for the end of the world because he wants to be remembered for generations as one of history's greatest monsters.
Toward the latter story arcs (e.g. when a new Endbringer designed to counter what they used to kill Behemoth appears), some readers have fallen into this state on the grounds that humanity is simply too overmatched by the evils that assault it. And this is before Scion decides to start annihilating everything in its path.
Fan-Preferred Couple: Almost any chapter with both Taylor (Skitter) and Dennis (Clockblocker) will have at least one, and probably several, comments to the effect that they should hook up.
Harsher in Hindsight: Knowing what is going to happen to the two sisters makes Glory Girl's interlude much tougher/sadder to read.
The reveal about just what Noelle can do changes how you read The Extermination Arc and Dinah's Interlude. Theoretically, the world's end almost started right there!
He's Just Hiding: Some fans reactions to the news of Battery’s death. Also, nearly everyone's reaction to Clockblocker's... disappearance.
Though the latter character did survive.
I Am Not Shazam: The title Worm seems to refer to Taylor/Skitter's abilities to control bugs, supported by a minor villain even referring to her as "the worm" at one point in the narrative. In actuality, the 'Worms' may refer to the reality-spanning entities that are the source of parahuman abilities... and are Omnicidal Maniacs to boot.
Kick The Bitch: The cold, systematic way Shadow Stalker is forced to watch as her life is destroyed is utterly horrifying - but she's such a vicious, bullying sociopath most readers agreed she had it coming.
Garrote. A Case-53 whose tentacles instinctively want to strangle any stressor. Points to trying to reach out through the internet to find a friend.
Bitch. Decidedly the Jerkass subclass: she's angry, hostile, anti-social, whatever you want to call it ... but only because she got screwed over by her power and she never had a real friend in her life.
WagTheDog. We knew from Interlude 19 (Donation Bonus #2) that she really wanted to become a minion to Bitch, but when we see her in 21.6, the way she lights up whenever she gets praise from Rachel and the way she sleeps curled up with Rachel ... she clearly came from some terribly-dysfunctional place.
Taylor herself gets this on occasion when life decides to screw her over. She's of the Iron subclass, but it's hard not to feel really, really bad for her past and the general hell she goes through, combined with her self-loathing. Indeed, even many of the people who ascribe to the Alternate Character Interpretation and say she's become a bullying villain herself at the end of the story still find her sympathetic, because she didn't entirely have a choice in what she became.