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.
Ass Pull: Pyro, introduced as one of the good guys in Ultimate X-Men, was inexplicably made into a villain in Ultimates 3
Complete Monster: Magneto, in a marked change from his usual Noble Demon status. Sometimes he makes Grant Morrison's Magneto look shy. For a start, though Retcon gave him his more familiar background, originally Ultimate Magneto came from a wealthy American family and was never on the receiving end of a genocide or any sort of prejudice, meaning initially he didn't even a Freudian Excuse for his actions and was even more of an arrogant dicknote the Retcon is that he was adopted, and did live through a genocide, though probably a more modern one than the Holocaust (that, or he is a liar). No Well-Intentioned ExtremistAnti-Villain as the mainstream one is, this Magneto is an abusive parent who once broke his own son's legs for challenging him; is a true mutant supremacist who believes that mutants should replace humanity rather than merely be protected from them (in fact, he's even implied to have been eating humans at different points); and has, on several occasions, attempted to eradicate the human race and rule over a post-apocalyptic mutant utopia in the aftermath as an extension of this creed. He is savagely ruthless to his enemies and, here, is the one who crippled Charles Xavier, because the latter had started to realize he was insane. He rules the Brotherhood of Mutants like a cult and encourages them to murder as many humans as possible, children included, and has organized several terrorist attacks with high body counts.
Crosses the Line Twice: Mr. Sinister shoving Xavier down a flight of stairs would usually be horrifying; except that here he does it while declaring that stairs are Xavier's Kryptonite Factor. This, along with the comedically deadpan manner he does it, cause the scene to become hilarious.
Darkness-Induced Audience Apathy: Most stuff leading up to, and following from Ultimatum, suffers from this, as the heroes are pricks, the villains are worse, the world is such a crapsack one that many want it destroyed as a mercy kill of sorts...
Ensemble Darkhorse: Pyro had very little screen time, only a few lines and didn't do much, but the fandom loved him. Until his character got derailed...
Fanon Discontinuity: Most of the stuff leading up to Ultimatum has had a less than stellar reception, in no small part because it takes Darker and Edgier to an absolutely ridiculous extreme.
I Am Not Shazam: Dazzler was originally the name of Allison's band, which she insisted on reminding people, but eventually became her codename.
Inferred Holocaust: Even though it is rarely mentioned, Stryker's camps imprisoned, demoralized, humiliated, dehumanized, and executed mutants they captured. After Kitty's bombardment of Utopia it has been implied that several mutants on Tian did not escape alive.
How about everything Magneto does, to unflinchingly attempting genocide of the human race, to kneecapping his own son? And the Weapon X crew, particularly Wraith? Wraith and Magneto don't cross the Moral Event Horizon, they are living, breathing Moral Event Horizons.
Mr. Sinister pushing Professor Xavier down a flight of stairs. That's just cruel, not to mention extremely petty. It also qualifies as a Crosses the Line Twice moment.
Narm: The way people treat mutants already caused some Fridge Logic in the mainstream Marvel-verse, but here the bigotry is made so outrageously over-the-top and rampant that it starts unintentionally crossing into Black Comedy (for example, at one point Ice Man saves a group of people from getting crushed by a falling Sentinel and not even ten-seconds after an old woman at least in her sixties chucks a bottle at his head and splits his skull open).
Nightcrawler, after he was turned into a homophobe, complete with an appalling Kick the Dog moment to poor Colossus. This was coupled with him becoming a Stalker with a Crush to Dazzler.
One could that this series is considered a Scrappy for the Ultimate Marvel universe due to it's wildly varying quality, absurd darkness, and being the lead-in to Ultimatum, the near-universally despised Dork Age of Ultimate Marvel.