Magneto's background as a Holocaust survivor is such a crucial part of his backstory that most writers are (understandably) reluctant to jettison it—but since the Holocaust happened in the 1940s, it becomes progressively less plausible with each passing decade that Magneto could be old enough to have lived through it while also being young enough to be a credible threat to the X-Men. The movies eventually tried to mitigate the issue by transitioning to prequel films that were explicitly period pieces, while the comics get around it by having him occasionally undergo regeneration processes that keep his body vaguely upper-middle-aged. As for Xavier and Juggernaut being veterans of the Korean War, or Storm losing her parents in the Suez Canal crisis, we just don't talk about that.
Happens to almost any major X-Men depending on the current writer. You can find runs where almost any character pretty much exists solely because the writer feels like they can't drop them, but gives them no actual relevance to the plot.
Mr. Sinister was originally intended by Chris Claremont to be the creation and villainous persona of a powerful psychic who was actually an eleven-year-old boy. As a result, he was given a rather silly name, vaguely defined powers with no clear limits, incredibly nebulous motives that frequently came across as For the Evulz, and an incredibly Obviously Evil design. He was meant to be a child's idea of what a supervillain would be like. However, as the concept ended up getting away from Claremont, Sinister ended up as a serious villain who just looks like that and chose that name for no particular reason.
Jubilee was one of the depowered mutants after the 2005 House of M event, but still stuck around as a superhero, initially as the tech-based hero Wondra, and then in the 2010 story Curse of the Mutants she became a vampire. While this did make her unique, the fact was that she really only became a vampire because Marvel wanted to appeal to fans of The Twilight Saga, which was en vogue at the time. It didn't take long for Twilight to fall out of public consciousness, yet Jubilee remained a vampire for years afterwards, making it seem rather odd when she would show up in other books, such as in Wolverine or various X-related books, when she herself quite obviously stood out from the other mutants with her mystical-based powers, and seemed like a bit of a relic of yesterday's news. Eventually, Marvel caught on to this. In 2018, Quentin Quire both cured her of her vampirism and restored her mutant status at long last.
A few early issues of the series initially implied that mutants got their powers from nuclear radiation, not unlike Spider-Man and the Hulk. This idea was quietly disregarded after a few short years, and later explicitly discarded (it turns out that mutants are just the next step in humanity's natural evolution, and their powers are a result of the Celestials mucking around with human DNA), but a few characters still have nuclear weapons written into their backstories as a holdover. Most notably: Charles Xavier still canonically grew up at a nuclear research center in New Mexico, and Sunfire is still canonically the son of a Hiroshima survivor.
Magneto continued to call his minions "The Brotherhood of Evil Mutants" long after his characterization shifted from Card-Carrying Villain to Well-Intentioned Extremist, making it clear that he doesn't see himself as evil. A few later writers have attempted to justify it by invoking the Then Let Me Be Evil trope: he acts like a monster because he was treated like a monster by humans.
Similarly, the X-Men were originally called "the Children of the Atom" because it was implied it was the experimentation with the atomic bomb that brought on mutations in the first place (Professor X specifically recieved his powers because his parents worked on nuclear research). As time went on, this piece of characterisation became Early-Installment Weirdness, and the X-Men became much more centered on genetics than nuclear physics, as well as retconning so that mutants like Selene, Apocalypse, the Forever Man, Burke or Wolverine have been alive since as much as prehistoric times, but the title was so iconic (As well as sounding pretty cool) that it's still used to this day. It was later Hand Waved by claiming that the detonation of the atom bomb just triggered a boom in mutant natality.
Reed Richards has the ability to stretch his limbs. However, as time goes on he used this power for actual combat less and less. Why? Because he's The Smart Guy of the Marvel universe, and that's dominated his characterization. If he shows up outside of the book, expect little use of the stretching, and inside the book only occasionally. Often he'll just be randomly stretched for no important reason, just for the purpose of them acknowledging that's his power or else he uses it to grab an item on a counter far away or something. Pretty much never for combat. Some more recent comics, such as 4, bring his elastic body back into the foreground by showing how useful such a power is when in the hands of the smartest man on the planet. His secondary powers from his plasticine skin (such as not needing to sweat, or enhanced heat resistance) come up often too.
In the same vein, there's his wife Sue Richards' codename, "Invisible Woman", which seems somewhat ridiculous now that she uses her forcefield powersfar more often than she uses her powers of invisibility. Her powers of invisibility are derived from her force fields, of course, but the writers have long since figured out that forcefields (which can also be used as force beams, and as Hard Light constructs) are far more useful in a fight than becoming invisible. This is at least partly due to Character Development: in the early days of the comic, Sue was much less of an Action Girl, and preferred to avoid the Four's battles.
Spider-Man is fundamentally a street-level superhero like Daredevil and originally his adventures had a realism because The '60s to The '90s was The Big Rotten Apple era of New York City (where real events like the 1977 blackout occurred in the page), a time of high crime statistics when the idea of multiple street-level superheroes in a single city had a little verisimilitude. Since the era of Giuliani and gentrification, however, street crime level has dropped down while highly restrictive gun laws have been put into effect. Of course, the presence and activity of supervillains don't depend on that for explanation, but fundamentally the reduction of crime should mean that Spider-Man's hero duties putting demands on his personal and professional life needs more justification than "it's New York".
The issues of gentrification and high costs in New York, the challenges to print media by digital media, and the rise of cellphones and the internet have also meant that Peter's old job as a photographer for a newspaper, being the guy who "takes pictures of Spider-Man", making a sufficient livelihood off of that (despite being lowballed on the price by JJJ), and still living in New York was harder to accept. It was already dated in The Oughties, that Sam Raimi's adoption of the same in the Spider-Man Trilogy came off to more than a few observers as Anachronism Stew (Raimi made it work however by artificially mixing different aspects of New York history). The Amazing Spider-Man (Dan Slott) had Jameson become the Mayor of New York, which essentially updated the dynamic between Peter and Jameson.
In the Ultimate Spider-Man series, Peter becomes a web designer (albeit initially entering the Daily Bugle with the photographs) and part of the plot had the Daily Bugle transition from a print to an online magazine. The Amazing Spider-Man (Dan Slott) then had Jameson become the Mayor of New York, which essentially updated their dynamic.
Likewise, the idea of "Peter taking pictures of Spider-Man" which is a beloved trope and central to his dynamic of JJJ suffers because Technology Marches On. In The '60s through The '80s, when all photography was done on film and professional photographs were shot manually with analog controls (i.e. selecting f-stop, exposure, ISO with fingers and in-camera in the middle of a shot), it was believable that a superhero like Spider-Man would be too fast to capture and needed an insider as it were to provide the pictures, which made it possible for Peter to gain exclusive rights to Spider-Man's still photographs. But this made it harder with the digital revolution and impossible in the smartphone age, as such the trope started fading in comics in The '90s and The Oughties and has disappeared in The New '10s.
Aunt May's original purpose was to be an unwitting obstruction in Peter's life for drama's sake: She was very frail so illness could strike at any moment, she didn't have much money so Peter had to get a job to support the family, and her constant worrying about Peter didn't mean sneaking out to be Spider-Man was tricky but kept Peter from telling her his secret (out of fear she'd die of shock). When Peter finally moved out of the house and was on his own he was free from her smothering while May herself was able to sell her house and move in with her friend, meaning she had a nest egg to live off of and had someone to take care of her. Later writers redefined her as a character. For example, The Amazing Spider-Man (J. Michael Straczynski) had her learn Peter's identity and provide him with much-needed advice and moral support throughout his run.
Gwen Stacy being killed off is treated by comics fans and other creators as a bold gutsy move to really drive home personal stakes and shake up the status quo by getting rid of a prominent supporting character and Love Interest. The reality is that Gwen Stacy was killed off in an iconic story, The Night Gwen Stacy Died, because the writer and many of its fans saw her as a bland Love Interest, a wet blanket girlfriend, and as such someone who was disposable and fair-game (the original plan to kill off Aunt May was vetoed). She was someone who liked Peter but hated Spider-Man and whom the writer Gerry Conway thought would be more interesting as The Lost Lenore than if she was alive, while the more developed and interesting Mary Jane Watson was established as Peter's real love. The problem starts when other versions, such as Ultimate Spider-Man and The Amazing Spider-Man Series decide to adapt the same story and situation, but depart from the original context (i.e. she was a bland character whose dynamic was more informed than visible) and make Gwen into a fleshed out and interesting supporting character, too valuable and attracting too much investment from the audience for her to be disposed of in a low-stakes storynote i.e. a story which is not intended to be Spider-Man's last adventure or major turning point a la Batman: The Dark Knight Returns or Whatever Happened to the Man of Tomorrow?. In the Ultimate comics, they killed her off gratuitously and then brought her back again much later as a clone-but-not-clone-as-good-as-the-real-thing, while the decision to kill off the highly popular and beloved version played by Emma Stone was seen as a stupid move since it removed by far the most beloved and liked character in the film (the plans before the planned sequel was canceled were copying Ultimate in reviving her as Carnage... and also an alternate universe Spider-Woman Gwen, years before Spider-Gwen was actually a thing!).
Almost all versions of Venom tend to give the character a white spider emblem on his chest, even though it's been decades since the Venom symbiote got expelled from Peter Parker's body and chose Eddie Brock (and later Mac Gargan and Flash Thompson) as its host instead. In its initial appearance, the symbiote had the chest emblem because it bonded with Peter shortly after his costume was severely damaged, and it took on the appearance of his Spider-Man threads because it (mostly) responded to Peter's mental commands at the time. Nowadays, the design thematically fits with the idea of Venom being a Shadow Archetype/Evil Counterpart of Spider-Man, but he had no real in-universe reason to look like that until the 2018 retcon that it actually represented the symbiotic dragons used by the eldritch god Knull that created the symbiotes, only resembling a spider coincidentally.
Iron Man's enemies can seem rather dated, specifically his Arch-Enemy the Mandarin as well as Crimson Dynamo, Unicorn, and Titanium Man, as his stories were originally heavily influenced by the Cold War when they were written. Since it ended, his foes have been more along the lines of the kind an industrial billionaire like Tony Stark would have, such as Iron Monger, Justin Hammer, Sunset Bain, Ghost, Whiplash, Blizzard and more. However, these old villains still stuck around, forcing Marvel to try to write them to fit current times even though they made little sense. Notably, Iron Man 3 completely reimagined the Mandarin as a front for the movie's realBig Bad Aldrich Killian. However, this was controversial, to say the least, and it was later explained that there still was a real Mandarin, who would go on and become the main villain of Shang-Chi and the Legend of the Ten Rings, reimagined to better fit modern times.
Star-Lord from Guardians of the Galaxy fame originally appeared in much older comics where he had, among other weapons and superpowers, a very special weapon called the Elemental Gun that could shoot one of the four elements from it. After the character was reintroduced in the Annihilation event and later the new Guardians of the Galaxy series, all the powers and weapons disappeared in order to turn Quill into a really experienced but otherwise normal human. However, for the next volume of the franchise, the decision was made to bring back the Elemental Gun and even have its lore expanded with more details about its origin and properties (and introducing two new elemental guns later). However, most writers missed the memo on this and continued having Quill using the guns as regular laser guns instead of his classic elemental function (The famous live action movie giving Quill a pair of regular space laser guns didn't help matters at all). Nowadays, the Elemental Guns are still there and Quill still has them. Despite them being used as regular laser guns most of the time, every now and then a writer makes a reference to how the weapons are actually able to shoot more useful and dangerous elements than regular lasers.
Tommy Shepard / Speed is an interesting case of an individual character actually becoming the artifact to a whole team. During the original Heinburg/Cheung run, Speed had some importance as a member of the team that was recruited from a high-tech security facility to rescue Teddy/Hulkling. Other than that, he was noted to have a strong resemblance to member Wiccan, who would later turn out to in fact be his twin brother in Avengers: The Children's Crusade. Much of his appeal came from being the Token Evil Teammate, as while technically a "hero" he often acted like a sociopath. However, once the original run ended, Speed was given practically nothing to do. He'd show up alongside the other Young Avengers, say little, contribute to fight scenes without doing much, but narrative-wise he had very little reason to be there other than to round out the team. Even in The Children's Crusade, it was largely about Wiccan, while the revelation that they were indeed twins played more into Wiccan's story than his own. Ever since the second Volume to this day, he stopped being a main character of the team. However, he's still considered part of the team by every writer who used the Young Avengers. There will always be a passing mention about how he couldn't make it to a team's reunion for various reasons or he will simply be there with the team but have no scenes or dialogue. He's easily the least developed and focused on of the original Young Avengers, something that quite a few fans took issue with.
Also, the name Young Avengers became a case of this ever since Kieron Gillen worked on it. The original name wasn't just to denote that they were young superheroes, but actually a take after the original Avengers with costumes, codenames and themes inspired by them note Iron Lad = Iron Man, Patriot = Captain America, Wiccan = originally Thor but later changed to Scarlet Witch, Hulkling = Hulk, Stature = Ant-Man, Speed = Quicksilver. Hawkeye and Vision directly took their names from their inspiration. When Gillen worked on them however, more than half the team were removed and replaced with America Chavez, Noh-Varr, Kid Loki, and Prodigy — none of them inspired by any members of the Avengers.note Although it could be argued that America became the new member inspired by Captain America after Patriot retired for good, Loki became the new member inspired by Thor, and Noh-Varr is part of the 'Captain Marvel' legacy, with Prodigy, a member of the New Mutants, being the odd one out. Nowadays the name lost even more of its meaning, given the existence of the Champions (who are both all-teenagers and mostly inspired by members of the Avengers), and the Young Avengers themselves have been aged to be in the range of 21-23 years old, which still young, it's not younger than what some members like Wasp were when they joined. Also, most of them have been part of at least one adult version of the Avengers by now which renders the joke of them not being 'the real Avengers' completely moot.
In the 1980s, Marvel decided to try codifying how strong various characters were in relation to each other, with a "Strength Class" system that topped out at 100 tons. It was very quickly apparent, however, that the system didn't match the actual events of the books; characters would routinely lift things weighing far more than a hundred tons, even ones explicitly supposed to be more in the 50-70 range. That said, while the tracking method turned out to be horribly off, the system did work as a way to establish who was stronger than who (characters who could lift 50 tons were almost always shown as weaker than characters who could lift 80, and those were weaker than characters who could lift 100), so the system stayed in place. Consequently, many sources use terms like "Class 50 super strength", without being all that clear on what Class 50 actually represents other than "more than Class 40."
During the mid-'10s, Marvel Comics had been pushing heavily for The Inhumans as the Suspiciously Similar Substitute for the mutants of the X-Men brand as the Randomly Gifted outcasts of the Marvel Universe, under the order of Ike Perlmutter to give the Marvel Cinematic Universe their own equivalent down the line, as Marvel did not possess the film rights to the X-Men at the time. This was seen as a massiveAudience-Alienating Era for Marvel, as the Inhumans were shoehorned whenever possible and the comics took every chance they could in downplaying the presence of the mutants. This culminated in universally-reviled stories like Death of X and Inhumans vs. X-Men, and not to mention the ResurrXion relaunch where they were shoehorned into sharing space as if the two were equals. All of this changed in 2019, when parent company Disney purchased 20th Century Fox in a historic $71.3 billion buyout, thus the film rights to the X-Men were returned to Marvel, and the X-Men were immediately treated as an A-list property complete with their very own relaunch. During this time, the Inhumans only got one miniseries called Death of the Inhumans, which ended with many of the new Inhumans Killed Off for Real and the classic Inhumans being Put on a Bus. However, Audience-Alienating Era as it was, this era introduced a number of Inhumans that are still around, such as Kid Kaiju, Moon Girl, Inferno, Lash, Synapse, Daisy Johnson (retconned into being an Inhuman), Blizzard (likewise), Toro (again), and biggest of all, Breakout CharacterMs. Marvel (Kamala Khan) who has become the most successful new hero in the '10s. Their origins are heavily tied to the Inhumans, and it's unlikely to be changed for that reason, and it looks rather awkward now that the Inhumans aren't being pushed in the slightest. They're a weird deal not being mutants, mutates, or any other origin, but rather a now-forgotten relic of time many fans prefer to forget, and yet there's no way it could possibly be retconned because it's hard-written into their origin stories (at least, not without some major and widespread finagling). Had these characters been introduced at any other time, they likely would've been mutants, if not something else.note Notably, Ms. Marvel was originally planned to be a mutant until the Inhumans push saw her changed to be an Inhuman, and once her Disney+ series premiered after the X-Men regained their full prominence, it actually went with her being a mutant, which eventually bled to the main series comics, where she was revealed to be a inhuman/mutant hybrid (a combination that was previously stated to be impossible).
The Punisher's status as a veteran of The Vietnam War fell into this over time—made sense in 1974, two years after the US started pulling out, not so much decades after, when Frank would have to be in his 60s or 70s at the bare minimum. Modern comics tend to either try to retcon it out, or merely refer to a nonspecific "war" he was involved in, but it never really sticks because so much of Frank's characterization is wrapped up in his history with Vietnam specifically. Punisher MAX is one of the more significant exceptions, as it goes so far as to actually portray Frank as an Old Soldier who's heavily greying and wrinkled. The Netflix series changed his background to the war in Afghanistan to be more contemporary.
occurred in the page), a time of high crime statistics when the idea of multiple street-level superheroes in a single city had a little verisimilitude. Since the era of Giuliani and gentrification, however, street crime level has dropped down while highly restrictive gun laws have been put into effect. Of course, the presence and activity of supervillains don't depend on that for explanation, but fundamentally the reduction of crime should mean that Spider-Man's hero duties putting demands on his personal and professional life needs more justification than "it's New York".