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.