Another theory, not necessarily about Peter's return, but about Otto's undoing. I remember hearing about a Teen Titans comic where Donna Troy came back to life (again) but this time she was based on Wally West's memory of her. Maybe Ghost Peter was Otto's memory of Peter. This memory of Otto's sort of gained consciousness because of Peter's leftover memories. He defeated Ghost Peter because Ghost Peter represented who Otto believes Peter was, inferior. However there might be an undoing in destroying his own memory in the process of deleting Peter's. Maybe he will have trouble in school, in the process of getting Peter's doctorate. His brain will slowly drain sort of like Tony Stark in siege or like with Doom and Dr.Banner. Losing his "superiority" in the process.
This could lead to Peter's return some how but that's another story. What do you all think?