They always have been, the X-Men were a metaphor on exploited minorities. Also, you don't understand what's actually Evangelion about. Is not about just metaphysics and philosophy, but a satire and puns on womanizing otakus.

The X-Men are the superhero comic version of the ACLU.

> The X-Men are the superhero comic version of the ACLU.

That's definitely what they are intended to be; however, I think that in practice they're closer to the superhero comic version of the NRA.

* Unlike real minorities, they have the power to quickly kill or maim those around them

* They're fiercely opposed to having to register their powers

* A lot of their stories are about how the only thing that can stop a bad guy with mutant powers is a good guy with mutant powers.