Folks have largely covered why the why this Mutants vs [Insert Team] thing keeps happening. Marvel has a real problem with this in general, and as someone said the mutants have far too many tools to utilize against any threat thrown at them. Those threats are often impersonal (awesome writeup by the way, this is a critical failing), so pathetic that they're quickly brushed aside by the mutants. The ridiculously long holding pattern Marvel has kept Orchis in makes it feel like they're keeping them ready for Hickman's wrap up to this era. They're a non-threat.
All the other various factions have fared even poorer, as noted earlier in the thread. Tune down the heroes, jack up the power levels of the opposition, and get some meaty personal conflicts with strong emotional cores going between the villains and heroes.