That is an awesome idea. To answer the OP I'll miss him as a Villain but not much else.I'm pretty confident that Doc Ock will return, as Marvel has killed him off before and they realized he was just too good of a villain to keep dead. Not to mention, we still have yet to find out what really happened to Doc Ock's body and who dug up and robbed his grave.
What I'm hoping for is Doc Ock will still retain all his memories of when he was in Peter's body, but, given how he's an insane megalomaniac, he might believe that Peter has ruined all the "opportunity" and "gifts" that Doc Ock "gave" him. He could even go into a classic villain monologue when he next confronts Spidey along the lines of: "I gave you everything, arachnid. A doctorate from a prestigious university. A company that was on the cutting edge of science and technology to rival that of Stark Enterprises that would've made you billions. Equipment that made you into the greatest and most efficient crime-fighter this city has ever known. The love of a kind, intelligent, beautiful woman. And you squandered it all! I see now that I misjudged you, Parker. The world was indeed better off without you in it. And because I gave you life, it is now my responsibility to take it from you!" To which Spidey respond with "Are you insane?! You stole my life! It wasn't yours to give in the first place!"
That's how I think Doctor Octopus could potentially become a villain again without getting rid of all the development he underwent during Superior Spider-Man, IMO.