Those characters are leaving his life. They're going to MIT and don't even know who he is anymore. This was absolutely designed to write them out of the story, on multiple levels. This Spider-Man will have a new status quo going forward.
I feel like they set up Ned to become the Hobgoblin. He no longer remembers his promise to not kill Peter Parker so he's primed to turn evil. Maybe him and MJ start dating and a battle with the bad guys ends with MJ dying and Ned blaming Spiderman for it.