Science Experiments gone wrong
One of the most common traits that spider-man villians share with their archnemesis is that they were given unique gifts through scientific means, though, unlike Peter parker, they do not see the responsibility that comes with their power. Doctor Octopus, Hammerhead The Lizard, The Green Goblin, not to mention the most recent additions to the Spider-man rogues gallery, the Freak and Paper Doll, all are accidents of science, and all deal with it in various ways.
Down on their luck
One of Peter Parker's most identifiable traits are his financial difficulties, a theme shared by many of the villains who, while super-powered, are primarily motivated by a desperate need for financial gain (or, in some cases, such as the movie version of Sandman, a sort of criminal altruism). The Scorpion, Vulture, Sandman, and recently, the Bookie and Thrasher are all examples of this phenomenon.
This is where the latest series of story arcs seem to have missed the mark. Much of spider-man's greatest enemies acted as father figures to him at some point: Norman Osborn, Dr. Octopus, The Lizard, all acted as mentors to Spider-man. Not only that, but during the Civil War, Peter tells Tony Stark that he has acted like a father to him, only to have that relationship come back to bite him in the ass, as Peter's unmasking (at Tony's suggestion) was probably the worst decision of the adult Parker's life. Say what you will about "Sins Past," the idea that your ex-girlfriend was boning your (spiritual) father represents a whole host of psychological issues that Peter has to deal with.
Or maybe I'm wrong. We'll see.