The key thing to understand is that Marvel is CHEAP thrifty and they would rather give opportunities to obviously talented but underused directors and actors than spend a fortune on someone that everyone knows is good.
Plus they have a pre-existing relationship with Joss on Runaways and Astonishing X-Men.
A lot of what Marvel is doing is convincing people to do their films for less (and signing them to multiple film deals) because being in a "cool" comic-book movie that makes a ton of dough will help their careers.
The Sylar story seems to be that he's an adict, and that he can't stop himself from grabbing new powers when he gets the chance. The flip side is that he currently seems like he maybe wants to try and stop, so that's (maybe?)