No, it's a comic book problem.
Magneto is talking like a crazy person. He keeps goading humanity's authorities as if he's not aware that they kill him in nearly every possible scenario/future. Newsflash, he's aware yet still talks.
Reed (and Doom) could wipe mutants off the planet, if they so choose, so why goad people on that level of multiversal genius?
Apocalypse earned his rep by dunking on every civilization that he encountered. people forget his humble beginnings. he's someone who has evolved to the point where he could have chats with the Watcher. and i just pulled this directly from wikipedia because i don't want to try to recap the story...
Apocalypse is later revealed to be back on Earth, no details about what the Celestials did to him were revealed, and is shown performing experiments to create an immortal vessel which he can then use as a host for his vast power and consciousness by utilizing a modified ancient Celestial technology known as the Finch, which can repair genetic decay. His efforts are not in vain, as he begins to impose his own consciousness onto a human test subject, the fourth attempt, lending it his own regenerative powers to withstand the assault. However, the test subject resists the process, causing a massive chain reaction that bathes Apocalypse and the subject in a wave of energy. Apocalypse's mind and body are torn apart. He finds his mind wandering to that of his birth before his being is fused, mixed, and exploded along with this human form. Once the wave subsides, Apocalypse finds himself in a strange new land that he deduces was the result of the explosion within the Celestial machine that must have caused a dimensional rift which threw him into another dimension. He also discovers that his body has changed as well. Not only does he discover that he can bleed, something that should be impossible with his injury-resistant mutant physiology, but after a fight against a resident of the twisted dimension, which he was able to defeat, Apocalypse learns that his body is actively refusing physiological mutation. Needing to breathe air for the first time in centuries, he comes to a shocking truth as he watches his hand turn from its usual mutated appearance back to a human form. He's becoming Human.[85] After degenerating into an ape form, he is taken out by his previous human test subjects who unlike him, had ascend in form after being empowered by Apocalypse's own DNA. He and other apes are tortured with the Finch, which was recovered and repaired by the human test subjects. When test subject D experiments on Apocalypse, he uses the last of his mutant power to try to transfer his mind into D and is finally able to possess him which restores Apocalypse to his former glory and realizes that he had not been transported to another planet, rather the earlier explosion from the Finch had simply evolved his entire South American island, infusing his superior genetics into everything the blast wave struck, transforming it into the tribulation which he had been forced to endure. Apocalypse then gave his perfect host body a trial run as he killed the remaining test subjects, while reducing the entire island to rubble that was reclaimed by the sea.
Superiors? Doom can literally destroy universes via his genius and he's a sorcerer supreme level sorcerer. Reed is even smarter that him, to the point that he could properly instruct a child into recreating different unique universes.
What is this debate? Mutants die pretty much every time, or they're killing themselves. They're no one's superior; just humans by another name.
“Strength is the lot of but a few privileged men; but austere perseverance, harsh and continuous, may be employed by the smallest of us and rarely fails of its purpose, for its silent power grows irresistibly greater with time.” Goethe