I dunno. . . when mutants where teenage runaways in pre-Giuliani New York, living in sewers because they were as terrified by society as society was terrified by them, that's when they were a metaphor for something. Most everything since then has just been a nod in the general direction of metaphor. With lots of explosions! And stabbings!
As for the other thing, I think they actually exceed the F4 for being cosmic heroes. The Shi'ar are now officially the dominant inter-galactic empire in the Marvel U, and they seem to have always had a mutants-only diplomacy policy with Earth. I agree that it's strange.