This isn't a hate thread about Superior, it's just a theory!
During the 80's, 90's and early 2000's Spider-Man was this tough guy, and he knew it. He could wreck teams and was incredibly competent and had a lot of respect from the Heroic community. Ever since 2005 or so, he's become the butt monkey of the MU.
Mary Jane during this time was also a strong character. Sure she couldn't fight crime and worried about Peter a lot, (can you really blame her? The man goes out to fight guys who could crack his his skull open if he held still for more than 5 seconds.) but she did things like beat the Chameleon with a bat, after realizing, very quickly, this wasn't her husband. Chameleon is a master of disguise this shows that MJ is pretty clever and knows her husband well. She and the husband even had a laugh about it.
Well in Superior we saw that she was reduced to a helpless damsel in distress, waiting around for Peter to come save her instead of trying to do it herself and she didn't seem to notice Ock's ego maniac tendencies, unlike Carlie Cooper.
We also saw in Superior Doc Ock was able to wreck Peter in his own mind, despite the fact he had the support of his loved ones and Ock one by exploiting the "fact" Peter is weak.
This isn't anything like Peter "Determinator" Parker like we've been reading about. Especially since just the thought of Aunt May was enough to give him the power to perform his most iconic feat of Will and to push beyond his usual strength early in his career.
Sure it may seem like I'm whining "RUINED4EVUR!" but I think there's a reason for all of this. It all dates back to One More Day, please hear me out.
Remember how Mephisto said " A part of your souls will remember and that soul will be tortured by your being apart from one another. (Paraphrasing). Yet it seems that Peter cares absolutely nothing about it and doesn't seem remotely fazed. Immediately afterwards is when "The Decline of Spider-Man" begins.
I propose that the Peter and MJ we're reading about are genuinely Peter and MJ, but only their "weaker" traits. That's why Peter's confidence is gone, and he's so easily out shined by Doc Ock. Mary Jane no longer the woman she once was, since that part of her character has been stolen from her.
Mephisto posses the Strong parts of their souls, and is torturing them, while making the "weak parts" suffer too. It's basically the same as taking the soul, just making them miserable. He's probably hoping he can drag the whole soul to his domain once they die. Since I don't think Mephisto could be fooled by a mortal.
It could be entirely possible that through Superior Spider-Man Dan Slott has set a plan to remove the weakness from Spider-Man. The Strong part of their Souls will come back to reclaim their bodies, once the deal is broken. Dan Slott is trying to retcon One More Day and put back ALL the continuity. The deal will be broken and then Peter will claim his body back. But that won't happen for a while, since Marvel wants to get what they can out of Superior first.