Reed Richards becomes a villain, the Maker, and makes a huge mess in Hickman's The Ultimates. He visited the prime earth back in Cataclysm: The Ultimates' Last Stand, realized the life he could have had, and had a HeelFace Turn. In Ultimate FF, he's still atoning for his actions. However, in The Avengers (Jonathan Hickman) and Secret Wars he's a villain again. Writer Revolt? No. He turned back to villainy when he opened his hearth to Sue, and she did not react just with a "Reformed, but Rejected" attitude: she tried to cut his stones with a forcefield scalpel to get the body fluids required for an artificial impregnation that would save the universe (long story...). So, Reed realizes that there is no point in being good, Sue will never accept him. Also, the mere risk of having your stones cut may have that effect on male people.
Most (If not all) of the Adaptational Jerkass may seem out of left field, but upon closer inspection, you realize that the characters are actually Deconstruction of mainstream counterparts: Professor X is a Manipulative Bastard, Captain America is a Noble Bigot from the 40s, the Fantastic Four fall apart because Reed became a villain from all the shit he went through, and so on and so forth.
Being a mutant has been outlawed in Ultimate X-Men after ''Ultimatum. We see the consequences on-panel, but the existence of that law means that several congressmen of both parties voted for it, and that the president signed it. And there is one more problem: the Equal Protection Clause. Even if legislators vote for this bill and the president signs it, it may be challenged in court as unconstitutional. After all, there is precedent: the Brown v. Board of Education case. But, as none of this happened... we can infer that judges are biased against mutants as much as most other politicians, to the point that their bias take precedence over their duties.