I think, aside from the fact that the X-Men are too busy infighting, the reason why the mutant allegory seems to have become blurrier over the years, is because the writers who did use this part of the X-Mythos tried to make it an all-encompassing metaphor for every kind of oppression that exists (race, gender, sexual orientation, etc...) which in return made it sound more hollow. Believe / like it or not, not every type of real life struggle fits the 'mutant as an oppressed group' metaphor.
There is also the fact that plenty of the most important mutants are cishet caucasian people who have never known poverty and live sheltered in opulence in a beautiful mansion, or go out shopping with wads of cash every once in a while. If you know anything about majority/minority power dynamics and the way race, sexual orientation, gender identity and class are related in most occidental countries, you know this isn't what oppression looks like (And yes, I know that the franchise is also truck-full of real life minorities but very few of them are nearly as high in terms of importance).
This is why I personally do not condemn the writers who apparently don't "get it". For instance, I get why X-Fans might be upset with the way Remender has handled the whole thing in Uncanny Avengers, but I can't blame him for seemingly missing the point. Writers who came before him kept appropriating real life minority struggles, and wash them of their significance and impact by making the victims of the acts the majority. I also do not blame writers who decide to ignore this part of the mythos that's becoming more and more convoluted and just use the mutants as a conduit to tell cool stories.