It's a really cool idea that doesn't get messed with as much as it should. They flirted with it a little after the run with stuff like bobby becoming all ice, but after that almost no one did stuff with secondary mutations, aside from the mothervine plot inducing artificial ones on mutants.
The main “secondary mutation” plotline I know of at the moment is everyone waiting for Ms. Marvel’s to kick in. Comes up in dialogue enough that I’m sure it’s building to something.
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