The Superior Spider-Man makes short work of the "new" Sinister Six with some prior planning.
Although Otto might disagree, the return of the Green Goblin probably made some fans happy.
Jameson declining protection and actually saving Otto in issue 12.
Otto and his minions curbstomping Shadowland. Kingpin has no doubts about which side will win the battle, and escapes.
In the Age of Ultron tie-in, Otto has had only minutes back in his lab when Ultron's drones arrive. Plenty of time. He's modified his spider-bots to take the drones over, then make them do the same to their fellows, stealing Ultron's army for himself (briefly).
"Firewall failure. System failure. System — system — superior."
Creating an army of henchmen.
Telling ALL OF NEW YORK that Phil Urich is the Hobgoblin and asking them to find him.
In issue #19, The silhouette of Ghost Peter forcing his way back into his mind, after Otto focused too hard on Peter's memories.
In issue #24, Mary Jane finally confronts Peter over what's going on. When she finds out about the Venom symbiote, she sics the Avengers on him.
Ock:[fighting off the Venom symbiote] I'm—I'm— Ghost Peter: I'm Peter Parker! I'm back! And this is just the beginning! Because, I swear to you, I will be... —FREE!
Issue #28: Mary Jane playing the role of the Wild Card and screwing up the majority of the Goblin King's plans.
Issue #29: The Goblin King hitting Otto where it really hurts: Blowing up the old Octavius home, the lab where he was first created, the place where all of his old inventions are stored, the bottling plant he saved and the heart clinic the he and Cardiac worked with.
Goblin King: Why, see here, if it isn't Chez Octavius? The house where you grew up. Oh, that's the lab where you had your octopus-related accident. And here's The Boneyard... where the police have all of Octavius' greatest inventions under lock and key. Look! The bottling plant that you as Spider-Man saved all those people from being blown up and guess what? They're all pulling a night shift. And what's this? The H.E.A.R.T. Clinic, where you dedicated so much time to helping the sick. An impressive body of work, Otto. A legacy any man would be proud off. Boom. Boom. Boom. Boom. Aaaaaand boom. HAHAHAHAHAHAHAHAHAHAHAHAHAHAHA!