X-Men does not make sense in a unified Marvel Universe. X-Men is a big broken aesop about how it’s wrong to discriminate, and mutant civil rights are conflated with minority civil rights (or, even worse, gay civil rights) as part of a big meta-narrative argument for why it’s wrong to fear people who are different. There are two major ways in which this falls apart. You can’t equate mutants with blacks or hispanics or whatever, because most blacks and hispanics don’t have the inborn ability melt a city block with the snap of their fingers. People aren’t scared of mutants because they’re different, they’re scared of mutants because they go flying zapping things with energy beams. People of different colors are more or less the same, y’know, we think, we feel, we have families, we do not have super powers.
Secondly, what is with people being okay with people who mutated after they were born to get super powers? It’s this second point that makes the unified Marvel Universe kind of stupid. Mutants are born with super powers. Sometimes these powers are dangerous, sometimes they’re lame. Regardless of their powers, everyone is all “Oh, noes, the mutants! I’m scared that my suburban living will be disrupted by their existence!” Never mind the fact that it usually is. (“Well, if there weren’t mutants running around, maybe mutants wouldn’t have blown up the _______!” The strawmen have a point.) But enter the Fantastic Four or Spiderman or some other guy who got his powers in a radioactive accident (hey, don’t those cause mutations?), everyone is all “Oh, they’re so great! They’re wonderful! Scientists, philanthrophists, blah blah blah!” Never mind that they’re for all intents and purposes exactly the same as people who are born with their powers.
So, yeah, it makes no sense to have a world where everyone hates people with super powers, except if they were not born with them.
Cirsova 
In regards to your first point: One of the things I loved about Grant Morrison’s New X-Men run was that he introduced a lot more mutants whose powers were harmless. It was a general trend among X-comics at the time – District X did the same thing. That meant that, yes, some mutants could fire lasers from their eyes, but most mutants just had a different skin colour, or could give tattoos without a needle, or other, similarly harmless mutations. Beyond that, the minority metaphor isn’t supposed to be exact. If it was, it wouldn’t be a metaphor any more.
For the second point, the heroes who got their powers as a result of an accident are anomalies. They’re not a new race, the way mutants are. That’s why other heroes can be loved while mutants are hated: Mutants are a different race.
I never really bought into the whole “Mutants are a different race” argument. I get where it’s coming from with the whole ‘next step in human evolution’ thing, but ultimately it comes off like it’s based on whether or not the radio active spider bit you in the womb.
I’ve got no beef with X-men. My problem is that it doesn’t mesh very well with the rest of the Marvel-verse.
I think this is why the whole argument in X-Men hasn’t really GONE anywhere in the last 50 years. They’re still fighting this equality war, still hated and feared because, you know, reasons. Well, and explosions.
Meanwhile, what the X-Men have allowed for are some of the most diverse characters in all of mainstream, DC and Marvel comics. It seems like half of the mutants are women (like they should be, you’d think, statistically), there are people of various races, all that. Throughout much of the rest of comics-dom, you have lots of beefy men and scantily-clad women. But in the X-Men, they can make people who are just sort of people, who happen to also have powers. Without having to compete to be the smartest man in the room, either, unlike all of the science-accident folks.
I guess my mind turned to this because of a long discussion thread over on this post: http://sourcererblog.wordpress.com/2014/04/14/top-10-marvel-characters-part-1/
You have a point, so long as you’re discounting Rob Liefeld’s run (which you should do for anything he worked on). Also, even though DC has gotten REALLY bad in the last few years, I feel like the first really pornified looking mainstream comic titles I’d seen were some of the X-men 4-part minis from the late 90s, early 00s.
I liked what Static Shock did with a similar premise: people weren’t wanting to round up the bang-babies because they were different, they wanted them rounded up and cured because they were teenagers who suddenly had super-powers. Also, most of the people affected were folks who’d shown up for a massive gang-fight. And when teenagers have super powers, you’d better believe that most of them are going to use them for some petty-ass-bullshit. Best villaing: the fat kid who used psychokinesis to steal food from street vendors.
Or you get something like The Incredibles which in a single movie does a better job of exploring these questions of how people would react to super-powered individuals than decades of comics do…
I loved the Incredibles because the the Incredibles was Watchmen without the crazy and without the rape.
Also, I know that X-men kind of tried to have this MLK / Malcolm X dichotomy between Xavier and Magneto, preaching the whole peace and co-existence vs. violent resistance, but it ended up slipping into Malcolm X vs Elijah Muhammad, with preaching “necessary” violent resistance in the name of equality vs. preaching wholesale violence in the name of supremacy.
Realistic, anyway, I guess… And some of it might be constrained by the whole super-hero-comic aspect, and about being part of that larger Marvel Universe. When what you have people doing in the universe, and what you have people buying the comics for, is super-powered combat… you have to deliver.
Lastly, in regards to your comment in that thread, “On the other hand, what else do you do? Solve their problems, smile, and end all your X-Men comics? Or turn them into Avengers 2.0? And lose all of the interesting sub-text and relevance?” Stan Lee had a history of losing writers because of his refusal to allow them to satisfactorily resolve character arcs, allow for ‘happy endings’ and make way for new generations. This most notably happened with the Fantastic Four’s run under Englehart, but cost a few others along the way, including Jack Kirby, who’d always intended to work in a Ragnarok storyline for Thor. Thank heavens he left and took his new gods with him to DC, or Superman would’ve never had any decent villains, cuz let’s face it, Superman is only good when he is fighting Darkseid.
These days they seem to be ending runs left and right. Restarting whole comic names. They even ended the Age of Apocalypse alternate universe! And now, in the midst of that, I would like to see more of the stories continue instead of end!
Which is to say, I have been enjoying a number of indie comics far more lately…
One of the side-effects of my long fandom of japanese comics is a desire for closure which western mainstream comics just didn’t (and really still don’t) offer.