@samirerre: claiming ignorance, asking for an explanation, and than telling the people who offer help you that they are wrong is trollish, and unbecoming.
These are Comic Books, not science. Stan Lee picked the word Mutant off the cuff in 1963, and slapped it on the series. Also, you can have both dominant and recessive genes that choose to manifest or not manifest. Blue eyes are a recessive trait, not everyone in a family will have blue eyes, but they will often all or mostly have the unactivated gene for it. At the same time there is a tribe in the Amazon where everyone has two toes on each foot. Still, this isn't the fictional X-gene works, so it doesn't matter.
The difference between The Avengers and and the X-men, going back to the 60s, is that the Avengers have always had known humans (Iron Man, Captain America, Hawkeye, etc) on the team, and because of that better PR. You don't get much better PR than Captain America. The FF have a known origin- the public likes them. For most of his history Spider Man was actually hated by many New Yorkers, in part because of a smear campaign by J.Jonah.Jamenson, and in part because many suspect he is a mutant. Mutant powers, in addition to representing a species based threat, tend to be less traditionally superhero based (in other words, the Superman package). My power is that every time I open my eyes everything in my field of vision gets obliterated by force beams, whether I like it or not. I smell act and look like an animal, have claws popping out of my hands, and can't be killed... not because the bullets bounce off my beautiful chest, but because you can watch as the exit wound closes up... to give an example. Wolverine is on the Avengers now because Marvel is shameless in their quest to maximize profits out of a dying whore, so don't go there.
As for plot holes, you try having multiple writers work on multiple series for 50 plus years, under some ridiculous editorial mandates, and have everything come out smoothly. That's why Marvelgrey told you to read 100-300... it's pretty much all written by one guy, so it has relatively few of these problems, even though an occasional editorial mandate did screw with things.
If you need more, read the wikipedia article.
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