Yeah, they left us with quite a cliff hanger. My bet is that the invisible guy will interfere with Sylar's brain slicing, then Peter will regenerate his broken flesh and fight back with all the powers he can muster.
So who wins in a fight between sylar and Peter if they have the same powers? Unless Peter has a power that Sylar hasn't yet stolen from him. Oh yea, the invisability thing Peter has might be helpful.