Arc Fatigue: A certain degree of this applies to major events such as Guardians of the Galaxy or Civil War, but Spider-Man takes the cake as it lasted two months. Events in general are one big case arc fatigue, as they're held back to back and exhaust players to the point that many simply don't care any more.
Author's Saving Throw: The game is not without its flaws, but one thing that most fans can agree on is that the developers are almost always trying to make things better for the players.
So far every event has had one, whether it be reducing the number of items required to obtain to reach event goals, making them easier to get, or restructuring how they work in order to make them easier to plan around.
Pepper's dialogue during the Rescue event, where she calls out Fury (and herself) for being so hard on Tony. This has been a sore spot among Tony fans because of how much he does around the Academy to help out and his character development across the game, so they were quite happy to see it addressed.
Baron Zemo. Some people think that bringing him to the academy adds an interesting dynamic to the characters, and might allow him to gain some character development. Others are offended at the fact that he is essentially A Nazi by Any Other Name. The same applies to the ability to recruit more HYDRA characters like Crossbones and Madame Hydra during the Civil War event.
Hank Pym is this and then some. While some enjoy his Crosses the Line Twice antics (such as electrocuting his students to improve their productivity), others despise him for exactly the same reason.
Jessica Jones being made a premium character during the Daredevil event. Many people responded with anger, given that she was heavily advertised in the buildup to the event; others expressed relief that she was made premium as opposed to another character like Punisher or Luke Cage.
The pure chaos of the final week during the Daredevil event. Many were outraged that Punisher, who could only be unlocked by defeating Kingpin 6 times, was going to be near impossible to get for most players due to the incredibly high difficulty of defeating Kingpin 6 times as well as the scarcity of resources needed to fight Kingpin. Players also had to unlock Luke Cage during the same week. With many fans having to accept they'd never unlock Punisher if they didn't pay a load of money into the game, it was a huge problem for the players. Many players announced they were considering quitting the game, while others decided they wouldn't take part in future events if things didn't change. Fans also getting the general feeling the developers didn't care and just want the player's money didn't help.
Ghost Rider being the first premium character of the Halloween event has had similar reactions to Jessica Jones. With indications that Blade will also be a premium... well the player base isn't exactly happy.
The Under Siege event, which promised to provide players a chance to get a number of characters from past events they might have missed. While they gave a number of them for free, it was made incredibly difficult to unlock the premium characters as they were only available through a special crate that required players to fight the bosses ten times to unlock (said bosses being incredibly overpowered while the playable heroes were limited per boss (Ronan only having three non-premium characters allowed to face him) and severely under-powered (with the method for levelling them up being extremely difficult) in comparison). The crate keys couldn't be bypassed by sharding either, so even if you were willing to pay-to-win, you didn't have the option. Making matters worse, even if you did get enough keys, you didn't get to choose which hero you unlocked, since it was completely random, which sucked for players who wanted one in particular. A number of players have found this event disappointing as a result, not helped by it being such a short event that you had a tiny window to go about the incredibly difficult unlocking method as it was.
Celebrity Voice Actor: As can be seen in the characters page, almost everyone is voiced by a celebrity. Most of the game's ad campaign relies on the A and B-List stars such as Colton Haynes and Alexandra Daddario, but there are also plenty of YouTube and social media personalities present as well. Those who don't have a famous voice attached are voiced by in-house VAs.
Loki dancing alone for two hours. Explanation A majority of Loki's missions involve him dancing at Club A for extended periods of time - often immediately after finishing a two-hour dance.
Steve has been working out in the quad for days. Explanation Steve takes a notoriously long time to unlock, mainly because his quest items (keepsakes) don't appear on very many quests and are often only rewarded one per quest. And while he's waiting to be unlocked, Steve constantly alternates between jumping jacks and one-armed push-ups in the quad.
Where's Hawkeye? Explanation Hawkeye was shown in the trailer and the promotional photos for the game, and had a voice actor announced shortly after release. However, aside from a few brief cameos, the most recent being the Doctor Strange event, nothing has been seen from him, leading people to wonder where he's supposed to be. Has become an Ascended Meme, as the question is answered in the FAQ.
Referring to the villains' prisons as "the shame cubes".
Rescued from the Scrappy Heap: Pepper Potts was much more well-received when she was promoted to a playable character because her storyline is basically a big Author's Saving Throw regarding to Tony that reminds Nick Fury that Tony is a good person and has admirable qualities as well as flaws.
There are quite a few missions that take four hours or longer to complete. While these can often be skipped, there are many story-related missions that are this length or longer and are unskippable.
Special events may offer loads of new content, but they come with harsh deadlines that many players struggle to keep up with, especially ones that can't or won't pay for the premium currency. Another issue is that TinyCo runs events constantly with little more than a day or two between them, causing fatigue; and while they offer regular event content they're neglecting promised content for the base game.
The original Spider-Man event was the third full-size event in a row (and if you count the British Invasion mini-event, it was the fourth in a row). Players were getting tired of the regular deadlines for event content and still adjusting to the fact that this was going to be the status quo from now on. On top of that, Spider-Man was double-length - basically two events one right after the other - which compounded the fatigue.
Multiverse caught flak because half the characters - essentially anyone not from 2099 - were no-name rehashes of characters that players actually wanted and possibly had already.
With Jessica Jones, problems came from the event's sheer difficulty. Factors that contributed to this included the fact that Area of Effect attacks received a severe Nerf just as the event started, and that the enemies were Hand ninjas that had already been proven to be Demonic Spiders.
They Wasted a Perfectly Good Character: Quake. She has the least characterization and variation of quotes among all the playable characters, which only emphasize her role as Naïve Newcomer (which got old pretty quick consider the fact you can upgrade her to level 5, and her missions revolve around her growing out of this, but her quotes continue to focus on this).
Taskmaster, to an extent. The game Adaptational Villainy removed many of his sympathetic aspect caused him to be flattened and lost nuance in quotes and interaction with the other character than he otherwise would have had.
Crossing into They Wasted a Perfectly Good Plot, but a lot of the event and bonus characters tend to have similar arcs-join to help fight the current threat, meet the cast, then grow suspicious of Fury and try to uncover his secrets, and form a team of some-sort for reasons. In a similar fashion the female spy characters all have similar stories of joining, being suspicious of Fury for reasons, try to uncover his secrets then fail, often interacting with other spy characters who either share their suspicions or have accepted he has secrets.
The Woobie: Tony is seen as this by many players. Though he has several moments when he's quite obnoxious, he also has many genuine attempts at being a better hero...which are almost always brushed off as annoying by Fury or Pepper.
Becomes even more pronounced as you progress through the game. It turns out Tony's smug superficiality is really just an act he puts on in order to cover up some severe confidence issues. While a genius in his own right, he considers himself a disappointment who will never live up to the greatness of his father.
All of the staff probably qualify, given that they're implied to have lived through the deaths of all their students in a previous timeline.
WTH, Casting Agency?: Since it was first announced, many of the voice options drew confusion from fans of both the Avengers and the actors cast. Many turned out to be surprisingly good choices, but some have proven to be rather ill-fitting. Gus Sorola as Hawkeye has been a particularly confusing choice as Gus sounds nothing like one would expect Hawkeye to sound, and once Hawkeye was finally in the game it was clear he used his natural voice.
Anvilicious: The series covers several heavy topics related to Post Traumatic Stress Disorder and Gender Identity primarily, with an odd combination of ham-handed and nuance. Post Trauamtic Stress Disorder, for instance, covers not just war, but assault and torture; and Gender Identity issues include bisexuality and whether or not the attempted sexual assault that awoke Striker's powers also 'caused him' to be gay.
Ensemble Darkhorse: Since joining the book as a background character in issue #21 Juston Seyfert seems to be rapidly becoming one. He even got a spotlight during the Avengers Vs. X-Men arc.
Although they ARE main cast members Mettle and Hazmat are easily the most popular characters in the book. As such fans were ecstatic when they finally got together. And they were really pissed when Mettle got killed off inAvengers Arena.
"Funny Aneurysm" Moment: Hazmat - an ethnically-Japanese girl with radioactivity based powers who has been described as a "walking Chernobyl". Less than a year after she was introduced, the Sendai earthquake happened, which caused radioactive material to escape from the Fukushima nuclear powerplant.
Juston and Sentinel's near-death experience at the hands of Emma Frost similarly becomes rather depressing given their fate in Arena.
Memetic Mutation: Mettle, particularly his face, became a meme on 4chan before his name was announced, where they called him "Fortress". Acknowledged twice in the comic itself, once of Mettle learning of his meme status (making up for him being mistaken for the child of the Red Skull) and later when lamenting the attention, he declares that they betrayed him.
During the flag football game Jocasta tries to keep order by using an in built taser to shock anyone who starts brawling, when Mettle is threatened with it he exclaims "Don't tase me, Jo!"
The Scrappy: White Tiger due to being a Canon Immigrant from a largely disliked cartoon and having a rather shallow personality that consists mainly of being a bitch and haranguing Reptil for not doing enough for the community as a Latino superhero.
Strawman Has a Point: During the "War with the Runaways" arc, Hank Pym and Tigra plotted to take Molly Hayes and Klara Prast and put them into foster homes where they would never be found by their older "siblings". Predictably, when the Runaways found out, they attacked. While Pym and Tigra's plan sounded cold and heartless, and while Hank Pym is probably the last person who ought to be making decisions about other people's lives, it's worth noting that the arc was, in part, a follow-up to the unfinished "Home Schooling" arc from the Runaways series, the central thesis of which seemed to be that Nico and Chase were god-awful parental figures who seemed especially ill-equipped to help Klara, who was still showing signs of trauma from her near-death experience and who is powerful enough to accidentally kill someone if she gets too upset. Thankfully, at the end, Nico casts a spell to make each team see things from the other team's point of view, and thus the two groups are able to reach a peaceful compromise.
The Woobie: Most of the cast, but Hazmat and Mettle in particular. Hazmat had her life and future ruined when her powers manifest in full, and she found out that some of the bad things in her life (sickness of parents, death of her dog) really were her fault. Now she's locked in a containment suit for pretty much the rest of her life so she doesn't kill anyone. Mettle's not much better off. It makes her very bitter, but deep down, she's very much a Woobie. Ever since he manifested his powers, poor he has shades of this. Looking like a monster thanks to his red metallic armor and having no skin as well as he was often mistaken as 'Red Skull's son' by the public. He is also qualified as the Iron Woobie.
Of all the instructors, it's Speedball. Though he is slowly recovering from his Penance phase, he still cuts himself behind closed doors as he claims that is the only way for him to use his more powerful, Penance-based powers in fights and he is haunted by the memories of Stamford disaster. This guy seriously needs a hug.