As for the Ezekiel&Morlun stuff, I would point out that, even within the storylines, it was always made clear that the mystic stuff was a possible explanation for Peter's life, not the definitive one. But since it was not well liked, it could have been used one last time in this way : Post-Civil War Peter is contacted by Ezekiel's spirit, who guides him to 'the web of his existence'. He says messing with this can fix up May and his ID, but he better be real careful. Also, using such a fundamental thing will shove all the mystic stuff way into the background to the point all the totem stuff will just fade out more or less permanently. In short, Peter begins playing with the web where he shouldn't, and this causes all the reset. Its still his responsibility, but now it is a failed effort rather than a surrender.