Adaptation Displacement: Blade. More people are familiar with the movies than with the comic book character, up to the point where Blade was all but turned into an African-American in the books to better match up with Wesley Snipes' portrayal. In the comics he was canonically African-English for years beforehand.
Archive Panic: According to Complete Marvel Reading Order, Marvel has put out some 17,000 "core" stories/issues in 50 years, or 22,000 if you want to include obscure stuff as well. And that's still discounting a lot of stories that are clearly out of continuity or just take place in the past, and the fact that they constantly produce new ones. Most of them can easily be read via Marvel Unlimited, but completionists obviously better not have a life.
Base-Breaking Character: Eddie Brock: Either a complex badass anti-hero who should be in more comics, or one of Spider-Man's greatest villains that became a boring, one-dimensional '90s Anti-Heroartifact that needs to just go away.
Continuity Lock-Out: Frequently, and is, along with the DC Universe, one of the biggest poster-franchises for this trope.
Dr. Pym can be an amazing character when written well, unfortunately so few writers know what to do with him.
Deadpool may as well be the poster-child for this trope.
Moon Knight, a lunatic with split personalities who flies around in a moon-shaped helicopter and regularly battles supernatural creatures.
Crosses the Line Twice: After Frank Castle killed third-string villain Stilt Man (with a bazooka shot to the groin no less) a group of other less notable Spider-Man villains held a memorial for their fallen colleague at a local bar. Frank made sure they were all there, then blew up the bar.
Designated Hero: A growing sentiment thanks to the "hero vs hero" Crisis Crossover event series like Civil War and Avengers vs X-Men, along with plenty of other morally dubious acts has led to many people finding it hard to root for many of Marvel's heroes (with the exception of more lighthearted ones).
Dork Age: Civil War and Avengers Vs X-Men. Some people are being quick to also add the 2016 Secret Wars (because of it ending the Ultimate universe and bringing its characters to the 616) and the second Civil War to this.
Ending Fatigue: The Hobgoblin's story went on for several years with two unmasking teases before picking a character who was already dead to be him (later revealed to be a fake 10 years later).
Amongst the villains: Batroc, Shocker, Baron Helmut Zemo, Mr. Negative, the Hood, Ghost, 8-Ball, Roderick Kingsley, and Boomerang.
Amongst the heroes: Blade, Deadpool (well, Anti-Hero more than anything), Hannibal King, Hercules, Darkhawk, Iron Fist, the Thing, Moon Knight, War Machine, Hawkeye, the Great Lakes Avengers (especially Squirrel Girl), Sleepwalker, Ms. Marvel (both Carol Danvers and Kamala Khan), Scarlet Spider, Venom, Agent Venom and Spider-Gwen.
With DC Comics, which is probably one of, if not the most famous fandom rivalry known to man. Debates on who has the better stories, who has the more well-rounded characters, which treats the talent better, and of course, the inevitable movie successes can get bloodied, and annoying for people who don't care about this sort of thing.
An internal one is developing from fans of the comics towards the films. While it's hardly the first time adaptations have influenced the comics, these fans believe Marvel is letting the films turn into a tail that wags the dog at the expense of drastically rear-ending previously established characterizations, storylines, and design elements, sometimes for entire series.
The complaints have been heavily against the way Marvel short-changes comics and brands simply because they don't have the rights to it, and the film studios that do have those rights don't want to give the goose that lays the golden egg. One controversial example is how the X-Men are transparently being downgraded in the Marvel Universe simply because of Fox's X-Men Film Series, while Fantastic Four, the comic on which Marvel was founded, was outright canceled (with some noting that it's analogous to DC cutting off Superman comics simply because his recent films have been weak). With the acquisition of Fox's properties and Marvel Studios confirming plans to integrate the two teams into the MCU, however, this is looking to change.
Fanon Discontinuity: Sam Wilson was never a pimp, ever. (As of All New Captain America this is the official canon, explicitly stating that the pimp origin as false memories implanted by the Red Skull to make Sam question his identity.)
One More Day for those who like the marriage between Peter and Mary Jane. Those who don't still deride it for how poorly written it was.
Storm/Wolverine (especially after the Storm/Black Panther marriage broke up on rather harsh terms), Rictor/Shatterstar, Rogue/Gambit, Peter/Mary Jane (after One More Day and in place of Carlie or Silk), Hawkeye/Mockingbird (instead of Hawkeye/Spider-Woman)
Non-canon: Professor X/Magneto, Iron Man/Captain America, Ms. Marvel/Spider-Woman, Thor/Loki.
Fridge Brilliance: Phil's descent into insanity and his FaceHeel Turn actually make a lot more sense than you'd think when you consider that people who take the Goblin formula often suffer from mental instability. Roderick Kingsley modified the serum he took so it wouldn't drive him crazy... but Phil wasn't so lucky.
Electro's star mask looks goofy to some people, but it's so distinctive and such an iconic part of his character that it's hard to imagine him without it. Even after he loses the mask, he gains scars on his face that have the same pattern. His Ultimate version really loses out for not having it.
Never Live It Down: Dr. Pym hit his wife once, and only once, while in the middle of a nervous breakdown. That never stopped characters from reminding him of that constantly, regardless of the context.
The Scrappy: Sally Floyd, Miriam Sharpe, Triathlon, the Sentry, Michelle Gonzales, Alpha, and Carlie Cooper. Wonder Man used to be this, but now it depends on who's writing him.
Unpopular Popular Character: Although he's come to be seen as something of a loser in the supervillain commmunity, the Shocker nonetheless has a sizable fan following. Ironically enough, it's his lack of a Freudian Excuse or obsessive vendetta with Spider-Man that make him stand out among Spidey's enemies. And as this profile shows, Shocker's actually defeated Spider-Man more times than you might think.
Mary Jane is this to the executive, as an inversion to Creator's Pet. The fans love her while the higher-ups would willing to ruin the franchise to get rid of her three times. One thinks they would learn from the reception of the first two.
Bob Budiansky wrote 8-Ball as a clever, dangerous criminal with a wicked sense of humor. Later writers made him yet another in an endless line of disposable C-List Fodder. What a fucking waste...
Jason Macendale basically lacked everything that made the Hobgoblin a good and unique villain in the first place. To illustrate how bad a villain he was, he once made a Team Rocket exit after a fight with Spider-Man when the latter was 'drunk!' It got so bad that Roderick had to come out of retirement and kill him to preserve his reputation.
Wangst: The Silver Surfer and Spider-Man slip into this when badly written.
Dr. Hank Pym. Jesus Christ, the shit this dude has been put through. First wife, dead. Second wife, dead. His robot son? Genocidal killing machine. The only robot son that wasn't genocidal? Killed by his genocidal brother. Best friend, Bill Foster, murdered. Other best friend, Scott Lang, was dead for a time and barely talks to him anymore. Just about anyone he ever cared about has wound up dead. He's had at least four documented mental break downs and all of his inventions have been turned to criminal use, tarnishing his scientific legacy. And all of this was before he was merged with the aforementioned killing machine, launched into space, and forgotten about. It doth suck to be Hank Pym.
The X-Men as a whole are a team of woobies, and the mutant populace by extension. Even the most upbeat and innocent characters like Nightcrawler, Kitty Pryde, and Pixie tend to go through a lot of hardship, while mutants as a whole have faced countless atrocities against them, including legalized enslavement and even state-ordered genocides. Its even worse for civilian mutants as they often don't have powers that are actually useful or even threatening (in some cases, they don't even have 'powers' at all, just physical mutations), but are stilltargeted for being 'freaks' by thugs and giant killer robots alike. Being a mutant means that you'll forever have a target on your back, but the 'cool powers' aren't a guarantee, and judging by the informed numbers of mutants compared to who we see, its a safe bet to say that most mutants don't have the kind of powers that can protect them from mob violence or giant robots.
Daredevil. It's basically fact that he has the worst life out of all of Marvel's heroes.
Shocker. One of the nicest guys around (for a supervillain) but nobody likes or respects him, not even his fellow supervillains. Add to that his tendency to get his ass kicked.
Awesome Andy, also known as the Mad Thinker's Awesome Android. After many years being the Thinker's goon, he was given freedom and became a worker at She-Hulk's law firm. He fell in love, had his heart broken, tried living a fake romance with Starfox's powers, got his heart broken again, and at the end of it all he simply reset his programming and became the Mad Thinker's goon again. It's hard to not want to hug the big blockhead.
Continuity Lockout: Due to all four shows sharing continuity, they have have at least a few episodes that wont make any sense unless you watched the other shows.
Western Animation/Avengers Assemble In particular has issues with this as it also takes a number of things from the MCU as Broad Strokes canon, despite the fact that they dont share the same continuity. This means the show will often forego explaining certain things on the assumption that the audience has seen the movies:
A big example is that J.A.R.V.I.S. disappears and is replaced by a new AI named F.R.I.D.A.Y. between Seasons 2 and 3. No explanation is given for this in the show, as it was a fairly significant plot point in Avengers: Age of Ultron. "The Kids Are Alright" establishes that F.R.I.D.A.Y. is the most advanced A.I. Tony created, leading to the implication that this change is the result of a system upgrade.
Early on in Season 4, the Wasp complains about the fact that her dad held her back and didn't want her to become a superhero. She's referencing the events of the Ant-Man movie (which like Age of Ultron, does not fit the show's canon), and not anything that ever actually happened in the series. In fact, Hope didn't appear at all prior to the fourth season, yet the show just drops her into the cast with personal baggage and pre-established character relationships.
Ultron is introduced in the series without any sort of context to explain him to viewers unfamiliar with the character or Avengers: Age of Ultron; the Avengers just know who he is. Not helped by the show dodging the subject of who built him.
The Vision is probably one of the most glaring examples. Unlike the other new Season 3 heroes (who all at least get some sort of token effort to explain who they are), Vision just sort of shows up and the Avengers are already familiar with him. (And yes, his voice actor is the one who previously voiced JARVIS.) The assumption seems to be that most of the kids in the audience have seen Age of Ultron and thus know his origin from there, even though there's absolutely no way that movie could be considered canon with the TV show.
The first example is how in USM and Avengers, Assemble!, the Guardians of the Galaxy originally shares the designs of their comic counterparts, however Guardians of the Galaxy cartoon would later be established to share the same continuity as the as the previously mentioned shows, doesnt make sense as their designs and personalities were designed to more closely resemble their MCU counterparts.
Season 5 of Avengers Assemble, "Black Panther's Quest" is a continuity nightmare. It's still officially listed as taking place after season 4, "Secret Wars," but several characters are missing without explanation. The crossover with Spider-Man features the Spidey of Marvel's Spider-Man and notUltimate Spider-Man (a change that also carried on into Guardians of the Galaxy)! The changed character designs are also the same as in Spider-Man 2017. When T'Challa meets with Attuma in Atlantis, he's a completely different character from the tyrant in Red Skull's Cabal in the early seasons. It's like the shows just hopped universes between seasons.
Fandom Rivalry: Averted. Even Marvel fans of the comics and the movies admit that in general Marvel animation hasn't quite reached the same level as DCAU and its animation spin-offs.
Avengers Assemble, like USM, has the burden of following a well-received Marvel show, in this case Earth's Mightiest Heroes. Season 1 was decried for too much focus on Tony (And his VA has also gotten mixed reception), a controversial version of Falcon, and female fans were incensed at how Black Widow was pretty much the only female character in Season 1, and even she was absent for several episodes. Season 2 has been seen as an overall improvement, with Widow now in every episode, Falcon getting a new and improved redesign and more focus on the team as a whole.