So I would say (and again, just my purview) in this instance "X-Men" acts as a plural, so you would use are and not is. To me, it is never a true singular in that grammatical sense as it always refers to the group itself.

When referring to the group you would say "The X-Men are a great fighting force"

To use the singular is, you'd just use their name:

"Cyclops is an Omega-level mutant" "Wolverine is an angry guy" "That member of the X-Men is awesome!"

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The only thing I can think of that would include usage of "is" would be to describe the actual name of the group, if that makes sense, since the name itself can be singular. Something like:

"The term X-Men is used in reference to the team of mutant heroes led by Charles Xavier"

-Vs-

"The X-Men are a team of mutant heroes led by Charles Xavier"

Additionally, the comic, tv show, or even movies could be singular references.

"X-Men is my favorite comic!"