What was important to Peter Parker at the end? Yes, getting his body back and beating Ock would have been best. An all-out sacrifice saving those he loved would have also worked. But neither of those things happened, because Octavius out-muscled and out-thought him on both fronts. Which makes sense, as they're both brilliant men who know how the other thinks.
When it became clear that neither of those things was going to happen, did Peter give up? No. At that point, it became paramount to not let Doctor Octopus run around in his body, using it to do evil as Spider-Man and Peter Parker. THAT ending would have been a huge middle finger to the character. Peter used their connection to show all of his most important memories to Octavius as Peter's life flashed before his eyes, in a sense bonding them to him, making Octavius really see things from another perspective.
Octavius, shaken and humbled, becomes a different man, and vows to carry on as best he can in Peter's name. He's still Octavius, of course--hence the "better than you ever were" moment at the end--but he's been diverted from his more sinister original intentions. He will try to be a hero. Peter wins, at least on that front, and it can be argued that's the most important one at this point.
And as for mourning, appreciation... Peter will get those things from Octavius. Not ideal, I admit, but it does work in an odd way, given everything that's gone down.
Regarding relations with MJ... well, I'm not sure how to feel about that, but it's been made clear that he's pursuing her on that front. I think it's less of a problem for me than it would have been if they were still married, but the OMD train wreck effectively nixes that. From that point to now, there's been the unspoken possibility of them getting together, but nothing solid--until, ironically, Octavius arrived. And while I get the squick factor in Octavius having sexy time with MJ, I'm thinking that this subplot is one of those tests for Superior Spidey's new character. I'm curious to see how it pans out, and really not sure what to think until then.
Regarding May... yeah. Weird. I'm pushing that out of my head. I'm sure Octavius will, too.
I think what makes this story much more palatable for me than OMD comes down to two points.
First and foremost, different and better choices were made by the hero. In OMD, Peter chooses to selfishly sacrifice his marriage to bring back his dying aunt, who by all measures should have been allowed to die. He just couldn't handle the guilt. It was one of the most un-heroic moments in the mythos, and was chiefly the result of a lack of testicles on the part of the editorial staff to tell some actually realistic Spider-Man stories in the wake of Civil War. It's what made me nerd-rage like I never have in the past.
Here, Peter doesn't take the easy way out. He fights, and never gives up despite the overwhelming situation he's in. And even when he knows he'll die, he still fights on, trying to convert Octavius into a hero. It is, in my opinion, one of the most respectful ways to have your hero handle that kind of no-win scenario. That he does convert Octavius is what makes this his final victory.
Second, this story didn't come out of left field, like OMD did. In OMD, May gets shot, Peter tries desperately to save her (which he should), and is (quite literally) magically shown there's nothing he can do to save her. All is lost, and then ALONG COMES MEPHISTO, offering a deal. It's Diablo ex Machina, with all the magic trappings thrown in to emphasize it. The editors wanted Pete and MJ's marriage dissolved, and quickly, and it plainly shows here. No respect given to that at all.
Here, this story's been building for quite some time. Clues and red herrings have abounded for the last 100 issues, from when Ock returned. If you look back to Spider Island, Ends of the Earth, etc., you can see pieces of the puzzle, and shudder at how they've been used in the most recent storyline. There was planning that went into this story, and it shows. You can not say that for OMD.