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: Ultimate Red Skull is even WORSE than the regular Red Skull. Ultimate Skull is the son of Captain America, and therefore has a version of his powers. He's a killing machine, although that doesn't sum up the sick delight he takes in what he does. His list of atrocities includes: killing two hundred people, followed by skinning his own face at the age of seventeen, training terrorists and working with numerous historical monsters, including infamous mass-murderer and cannibal Idi Amin, shooting Kennedy, just to send a message, and using the Cosmic Cube to force the members of A.I.M. to eat each other. And then there's his most infamous moment: he gives a woman (later the Red Wasp) a Sadistic Choice: kill her husband with a pair of scissors or he'd kill her baby. She did it. The Red Skull then chucked the babyout a window and let his three thugs gang-rape her.
Crowning Moment of Awesome: Surprise! The Iron Man Six armour! This is after he found out that Natasha was a spy - he found this out by her killing Jarvis - and that terrorists had invaded. He responded by whacking her with a bottle, getting very, very drunk, and launching, in his regular armor, for the space station. His next appearance is in the Iron Man Six armor, laying waste to the Crimson Dynamo robots.
Hawkeye's escape scene in Grand Theft America where he kills a room full of soldiers by ripping his fingernails out and flicking them at them. Did I mention he was strapped to a table whilst doing this? Followed up by his turning to the security camera which had just seen him doing this, and grinning a Slasher Smile: "Run."
Darkness-Induced Audience Apathy: The first couple of stories averted this, being seen as a good take on pre-existing comic stories. Afterwards, it seems that Jeph Loeb seemed more concerned with just making it Darker and Edgier, without any good reason or paying any respect to the canon.
Don't Explain the Joke: Nick Fury saying that Samuel L. Jackson should play him if there was movie about him is a little too on the nose, given that Fury's appearance is already based on Jackson's.
Fridge Logic: The DNA-specific bullet. Ultron calls this whole thing a crime of passion, and he apparently only shot Scarlet Witch the moment he saw that she and Pietro were lovers. Yet he'd been carrying a bullet coded to her DNA around all this time? Also, said bullets never showing up again.
Ultimate Hawkeye is a violent sociopath with the ability to turn any thrown object into a deadly weapon, making him an Expy of Daredevil antagonist Bullseye. Years later during Dark Reign, Norman Osborn has several villains take on the identities of the Avengers; guess who Bullseye disguises himself as?
A minor example, but the introduction for the hardcover collection of the first series happens to be written by Joss Whedon.
Magnificent Bastard: Captain America will regularly perform incredible combat strategies that are calculated within seconds, and stated outright that he seems to have "always winning" as an actual power. He will simultaneously sprout callous (from anybody else extremely arrogant sounding) Jerk Ass sentiments while performing them.
For Ultimate Reed Richards, if orchestrating the city consuming Germany was not be enough, then assassinating the president by blowing up Washington D.C. definitely counts.
Never Live It Down: In the mainstream Marvel Universe, Hank Pym only hit Wasp once and he wasn't really himselfat the time. In this continuity, Hank is a straight-up wife beater. In fact he goes further- when Wasp tried to get away from him by shrinking down to miniature size, he got even more furious with her and sent an army of ants on her- remember, she had shrunk, so imagine how close this came to killing her.
Nightmare Fuel: Okay, the argument between Hank and Janet, as noted under "Never Live It Down", was bad enough on its own, but unleashing a whole ant colony towards a shrunken, naked, stunned, and helpless Wasp? No. That's just Sick and Wrong. Seriously. Janet's horrified "HAAAAAAAAAAAAAAANK!" isn't either narmy nor hammy, but completely justified. The equally horrified look on her face, combined with what the experience must have been like (that is, from her point of view), is bound to take you off-guard, regardless of what your age is.
Villain Sue: Gregory Stark who emerges in New Ultimates vs. Ultimate Avengers as the Big Bad, has tech supposedly far superior than any of the heroes (many of which are with Hulk powers, is positioned as The Chessmaster better than even Nick Fury, and essentially wins despite dying while the heroes talk about how better things are because he did.
The idea to make Ultimate Captain America display Deliberate Values Dissonance attracted a lot of controversy even before they famously took it into hamhanded directions, since his mainstream counterpart is famously portrayed as being forward-thinking, idealistic and enlightened for whatever era he's in.
The All-New Ultimates take on Jessica Drew, from the costume to the new alias. A lot of people aren't happy with the changes, which is even easier to notice since she was a big Ensemble Dark Horse before the series started.