I don't think Heroes has really jumped the shark. I think things are getting a bit convoluted and messy and that Peter is having a hard time figuring out who to trust since he's seen the future. I think it's getting pretty damn obvious though that Noah is going to lead the Heroes against Peter's dad (can't remember his name) and the Villains by the end of the season.
I am starting to wonder how Peter's going to get his powers back though (maybe an injection?).