GhostPeter's Moment of Weakness, interfering with Ock's attempts to help to girl to prevent Ock from finding out about him. Peter would NEVER risk anyone else's, especially a child's life to save himself... if he were really himself. However, GhostPeter has been subtly holding Ock back from going too far since the series began, who's to say that it isn't going both ways? As GhostPeter was making Ock into a better person, the opposite is true, Ock is making GhostPeter into a worse person.
He's also in the King of all F'ed up situations, it's understandable he'd start to break under the strain and start doing pretty desperate stuff.
In the early issues, JJJ was Spider-Man's biggest supporter... when he had actually become a menace.
Otto's hatred of clones (referring to them as "abominations" and "mockeries of humanity"), answers a fan question about why he didn't simply clone a healthy body and transfer his brain patterns into it after finding out he was dying (Not an unfeasible premise, considering the myriad of cloning tech found in the Marvel universe). He would consider the clone a worthless "copy" and not his real self.
Surely the Avengers & Peter's loved ones would figure out that it isn't really Peter Parker they're talking to after a conversation or two of the guy acting like a completely different person.
According to Word of God, they think he's just acting like a jerk, but don't suspect he's not Peter. Word of God did say that he would be avoiding anyone with telepathy.
Depending on the Writer - Mary Jane (As written by Dan Slott in Superior Spider-Man) hasn't figured it out but suspects that something's up, having called Peter out on how he's been behaving lately; but Wolverine (As written by Chris Yost in Avenging Spider-Man) figured out that something was wrong with Peter within minutes.
Even if this thing gets undone, Otto has full access to Peter's memories. Not only does he know his Arch-Enemy's every secret, he also knows the secrets of every single superhero Spider-Man ever befriended, ever shared secret identities with, ever teamed-up with or even fought against - everything he learned, Otto now knows. If we're gonna see the return of Doctor Octopus, he is going to be far greater threat than ever before.
Thankfully, this is easily rectified. Tony Stark has mindwipe tech, even if all the mutant and Avenger telepaths are conveniently unavailable.
There is the possibility of Otto staying good even if the swap is undone.
After Otto's killing of Ghost-Peter, that's looking less and less likely with each issue. Unless you happen to think that blackmail, mass destruction, and an army of Mooks are hallmarks of superheroes. But on the bright side, he also no longer has Peter's memories. The fact that he doesn't and tries to get them back is why Pete is coming back again slowly.
Resolved. Octopus has been erased... at least for a while
Recall that Otto still has feelings for Aunt May and now he's her nephew.
If the switch does get undone, Peter will have to deal with even more crap since it's unlikely that the public will know it ever happened. MJ going out with some other guy, Otto wasting his Aunt May's money away along with many other people's money, Black Cat hating him now, Otto making him lose his reputation at the university, the Avengers lacking trust in him... Maybe he really is better off dead.