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.
Arc Fatigue: The Apocalypse Twins/Kang storyline started in issue #6 (with a prelude in #5) and ends in issue #21, for a total of 16 or 17 parts depending on how you count.
Ass Pull: Jarnbjorn. Seriously, so out of the blue Thor is able to enchant a weapon to easily kill Celestials? Keep in mind, these are the same beings that his far more powerful father with several thousand years of preparation, an armour that increased his strength even more and the power of his whole Pantheon backing him up couldn't endanger more than a helpless child. Especially jarring is that it can one-shot Celestials, but only injure Apocalypse.
Broken Base: Fans are split over whether Wanda is a Karma Houdini for her role in the original depowering of mutants. Not helped by the fact that the comics have offered several different explanations of why it happened in the first place. It's also not helped by the fact that In-Universe and out, Cyclops is currently being condemned a terrorist for actions which are both considerably minor in comparison though at least similar, and are actually directly the result of her depowering mutants. Considering Wanda herself has criticized Scott for what he did and gets treated as a woobie any time anyone tries to call her out on her actions, MANY are finding it a massive Double Standard.
Rogue and Wanda's apparent deaths have left a bad taste in many a reader's mouth. It does not help that they were the only mutant women on the team.
Complete Monster: The Red Skull. As if stealing Xavier's brain wasn't bad enough, he plans to cause the mutant equivalent of the Holocaust with it and become the Red Onslaught so he can rule the Earth as he fancies.
I Am Not Shazam: The team isn't actually called the Uncanny Avengers. The actual name is the Avengers Unity Squad, while the title of the book is just a callback to the long-running Uncanny X-Men series.
Like You Would Really Do It: Issue 14 features no less than three main cast members apparently meeting grisly ends. The fact that one of them will be in an upcoming movie, another appears on the cover of an issue three months later, and the involvement of Kang and other time travelers leave the fandom doubtful any of them will stick.
Taken Up to Eleven in issue 17, where the death of Captain America is immediately followed by the destruction of Earth and all its inhabitants. Yeah, that's going to be permanent.
Magnificent Bastard: Kang, who manipulated his adopted Apocalypse Twins, the Avengers Unity Squad, and a bunch of people from different time periods in his quest to gain omnipotence.
Memetic Mutation: With Charles Xavier's brain The Red Skull will eliminate mutant menace!
Never Live It Down: It may seem as if everything that Wanda did in the past was depowering mutants.
Speaking of brains, what The Sentry does at one point to restrain Wasp, after an attack badly damaged his body. Ew.◊ Thank you very much, Thor.
Avalanche's brain surgery
Only the Author Can Save Them Now: Assuming the series will have any sort of ramifications on Earth-616 now that Earth was destroyed in Issue #17 and doesn't take place in an alternate universe, the Apocalypse Twins arc has to be retconned if its going to be consistent with the other ongoing series taking place in the same universe.
Unfortunate Implications: Havok's speech in issue 5 (as written about by Comics Alliance, Newsarama, and Comics Beat) where he denounces the word "mutant" as "divisive" and that "represents everything (he) hates." Particularly difficult considering how mutants have long been written as representative of minorities in real life, creating the image of minorities being told to assimilate and abandon the idea of identity politics if they want to avoid persecution. Remender's intent is to have mutants be treated as every other super-powered individual in the Marvel universe, but the wording of the speech makes it very YMMV. NOT helped by Remender telling complainers to 'drown in hobo piss' afterwards. In addition, compare Havok to a Morlock and you'll see that it doesn't fly on the assimilation routine. He can pass as a handsome blond-haired blue-eyed white male if he takes off the costume, not to mention he's trying to speak as the leader of mutants or a figure head, which he's not considering the Unity Squad itself is a poor representation of said Unity when you remember that mutants have been helping the Avengers for a long time and it hasn't swayed opinions. Doesn't help that Brian Bendis was quick to give it a Take That over in All-New X-Men, where Kitty essentially calls Havok a dumbass.
Havok having half his face burned off by Kang recently and now terrifying ordinary might be a way of having any talk of "assimilating" be put to rest.
Villain Sue: The Apocalypse Twins. Able to effectively one-shot a Celestial. The same beings an Odin-possessed Destroyer armor couldn't lay a scratch on. Even though Uriel was killed, Eimin prevents Thor from slaying Exitar, which leads to the destruction of Earth.
WTH, Costuming Department?: The Scarlet Witch, who used to be the Avengers Ms. Fanservice (see here), now uses just an all-dark red suit (see here◊). Justified somewhat by her now being far more reclusive thanks to guilt from what she did to the mutants and others making her more wallfowerish, and as such unwilling to show off her body so openly. Its also not really an issue if you don't care about (or even prefer) seeing female characters covered up or wearing practical outfits.