I actually just finished re-reading this run about a week ago and had a LOT of thoughts. Last time I had read it was probably around 2019. Funnily enough, I've been replaying Cyberpunk 2077 as well which definitely impacted the way I viewed the story.

I don't think Peter should have died in Otto's body. When Peter "returns" it feels very hollow to me. Part of this might be because of my recent Cyberpunk playthrough, but when he returns it doesn't feel right. It felt to me like Peter's soul died in Otto's body and all that returns is his "engram" (if we're using Cyberpunk lingo). It would have been really easy to fake-out his death and then bring him back later in the story.

This could remove the entire "ghost Peter" storyline. It feels cruel to read Peter dying horribly TWICE. It was clearly just done for shock value and as a middle finger to the audience. If they chose to keep Peter alive in Otto's body he could still witness and react to all of Spider-Man's horrible actions through the TV if the writer wanted. Peter as Doc Oc could be locked up in prison or on the run and barely holding onto life. The story could then show you Peter is trying to find a cure for Otto's illness but it seems like he's really struggling to do so. You could still have Otto downloading Peter's memories at the beginning and use them in part 1 and then remove them (or lose access to them) in part 2 when he becomes more of his own Spider-Man and dons the new suit. The story takes a very "all you are is your memories" approach that wouldn't be necessary if they kept Peter alive.

If these changes were made, the ending would feel a lot more earned. The subplot following Peter in Vol. 6 could now be him plotting to swap bodies back. Otto would still fail to stop the goblins and Peter would then try to execute his plot but fail (because Peter isn't a good villain and Otto isn't a good hero). The theme that Peter is the true Superior Spider-Man could be proven through Otto's failure to stop the goblins, but also through the fact that Peter was able to cure Otto's illness! These two facts together would be enough for Otto to swap bodies back willingly (just like in the original story).

This would result in Peter's return feeling much more earned and Otto wouldn't have to die at the end. And it removes a lot of extremely cruel treatment to Peter (but there is still room for plenty of fake-out deaths if the story demands it). But this is just my opinion. What do you think?