Consider the Civil War storyline, in which Captain America leads a group of superpowered individuals resisting a law that would require them to register with the state and get some training in the use of their powers. We make people register when they purchase a gun. We don’t allow them to purchase missiles. We’ve considered attacking North Korea and Iran to delay their acquisition of nuclear weapons. And you’re telling me that Michael Bloomberg has no legitimate interest knowing that there’s some 12-year-old with anger management problems and an abusive father who could accidentally wipe out half of Manhattan?
If there’s to be peace between humans and powers, a sense of personal responsibility and some key leaders talking up peace won’t get it done. But perhaps greed will. In the current Marvel Universe, genetically enhanced supergeniuses spend most of their time inventing weapons to fight one another. In the real world, Hank McCoy would get really, really rich. In the real world, Storm would run a weather consulting business in which governments and giant agricultural firms would pay her enormous amounts of money to end droughts.
The battle lines in the X-Men series are between mutants who believe they can coexist with humans and mutants who don’t. I suspect that the real conflict would be between mutants who can benefit, either personally or financially, from the status quo and mutants who don’t. Species war is bad for profits, after all. Xavier, to his eternal discredit, lets his dream of peace be defined by Magneto’s dream of war. A dream of shared prosperity would be better, and stronger.
Another option would be nationalism. The Watchmen comics handled this well. Dr. Manhattan was a terrifying weapon of mass destruction, but he was our terrifying weapon of mass destruction, and other countries were weaker for lacking his gifts. I suspect you’d see something of an international arms race to cultivate and attract powered individuals, and that’s a race America would be well positioned to win.