Pretty much none if you're talking about powerful microwaves. The problem is that it's physics. Microwaves break the bonds in molecules (mostly through heating). Unless the mutants are made out of diamonds it gets hard to resist the eventual breakage.

However microwaves, or any radiating wave, diminishes by the inverse square law. Which means doubling the distance reduces the radiation by 4 times (or put another way; it gets reduced to 1/4th of the original). So the best mutation against a weapon like this is called GTFO.