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My philosophy is the more the merrier and that includes all teams and characters. And as far as the X-Men are concerned, there is no way they will not be included (now after the rights are back) in a Marvel game that is not specifically Avengers or Fantastic Four, etc.
Now that their film rights are back with Disney/Marvel, they will most likely be the next big franchise after the Avengers and begin to dominate the comic landscape much like the Avengers have since 2012.
Popularity is usally something that rotates, so I am not too worried about a particular group "taking over". I for one am happy that the game incorporates so many facets of of the greater Marvel universe.