In my opinion that's retconning, the introduction of ideas used to explain stuff that had already been around for years. The main reason is probably because somebody at Marvel thought it would be a great idea to make mutants be about hate, bigotry and discrimination. An idea that has become tiresome after all these years. Yes, Stan Lee thought it would be a good idea to introduce heroes that were hated instead of loved just for the sake of variation. These were the early days of the Marvel universe where consistency and inner logic were not taken as seriously as today. And the early Magneto was a wannabe Hitler who meant mutants were superior. But that concept was eventually abandoned and what we got instead was a team of superhumans who were bonded together because of the origin of their powers and the fact that they all went to a school to learn to master them.
Also, if there is an organism like Sublime that is affecting human behavior, the whole "hate, bigotry and discrimination" allegory falls flat because it takes away your free will and turns humans into puppets of a "higher power" for the lack of a better description, that don't hate mutants, but consider them just an obstacle (but not a threat to its existence), the same way someone who can't digest lactose consider dairy products an annoyance. The metaphor for racism doesn't work either. Racism is represented by someone from the outside, people of a different background than yourself living in the same area. Mutations are cased by changes from within, not from the outside, even if radioactivity or some other mutagens are required to trigger the mutations in your own genes, which you then pass on to your children.
The only difference between mutants and superhumans like Fantastic Four, Hulk and Spider-Man (forget the Spider-totem nonsense) is that mutants were born with their powers. According to Lee, he got the idea after all the testing of nuclear weapons, where radioactive particles would become part of our atmosphere and the air we are breathing, triggering mutations in humans who would on some occasions give birth to mutant babies. There are two types of mutants; those who are born from parents that already has superpowers themselves, like Franklin Richards, and those who are born from parents without powers.
But later on being a mutant became something more. Originally there were no more mutants than you could count. They all had a specific name and power. Then we were introduced to the morlocks, and suddenly they were too many to count. And then, due to some genetic countdown, there were suddenly millions out there. Also something about secondary mutations, and how Vargas, a superhuman born with powers, was not a mutant but a part of humanity's immune system against mutants.
After Scarlet Witch turned the majority of mutants into non-mutants, there was born a baby some time after that. A baby born with "the X-gene". Not
a mutation, but
THE X-gene, whatever that is. Probably the same gene that makes mutants immune to the Techno-Organic Virus from the Phalanx and Sublime. There are also viruses targeting specifically mutants, but not superhumans in general. As for the Sublime virus, it doesn't make that much sense. It's a virus infecting all living creatures. Humans are just a small part of all the life on earth. There are plenty of others; arthropods, protozoa, fungi and plants and so on, it can infect and probably does. No reason to be completely dependent on a single primate species. Just because you are allergic against peanuts doesn't mean you can't eat all the other food.
A mutation meant that you were born with a different genetic profile that manifested itself in either powers and/or a different body. You were born with it, that's what the mutation meant. Now being a mutant means something more, even if it is never explained. That's why they talk about "mutant powers", instead of just being born with specific superpowers. Are Angel's wings a mutantpower? Of course not. What about Beast's body? In the movie his hand turned human once it got close to Leech, which was absolutely ridiculous. The same thing happened when Wolverine and Beast was captured and sent to a prison for supervillains. They were given a collar that removed their mutant abilities. Wolverine's sense of smell and hearing were probably a lot weaker, but the silliest thing was that Hank got his human body back, as if being a blue gorilla was a special power.
Other than that, the distinction between humans and mutants is artificial. Mutants are humans, but they are humans with one or more talents others don't have. It is not the powers themselves, because other superhumans have them too. It is apparently the fear of being replaced. But older generations have always been replaced by younger generations. If those generations have extra powers, then so what. It's not who they are, but the fact that their powers can be passed on to new generations. Which parents wouldn't want the best for their children?
In the real world there is no such thing as next stage in evolution from one generation to the next. It is mutations combined with natural selection over longer periods of time, and the evolution is a blind process, even if it is something possible to predict the evolutionary direction.
