1. Supervillains becoming too heroic It works in some instances, but when you do it too much you run into a situation where you're reforming iconic villains faster than you're making them, leaving only new unproven villains or villains no one cares about. (see Xmen).

2. Every villain having some kind of deep connection to a hero.

3. "vigilantes" being treated differently than traditional superheroes. What is the difference exactly? Does the existence of superpowers somehow make you less of a vigilante?