In "Brave New World", Peter flies at Samuel. Noah and Claire even talked about it (Noah: And all the other stuff-- Claire: The flying, the rumbling--), so it really happened. How is that possible with Peter's current power? After all, since "The Wall" he's had Parkman's ability, and after the flight, he takes Samuel's power.
Sure, he could have hooked up with West again, but... what is the likelihood of that? Did Sylar possibly have an ability to fly that he could have taken?
Of course, I would rather like to think that his original power is finally returning.
And while we're talking about Peter and his powers: why hasn't he ever taken Sylar's one true power? Is it because of the hunger, as we saw on third season? As we also saw there, Sylar was capable of same kind of empathy as Peter, which didn't require him to get all touchy-feely with the brain to know how it works...
Oh well, either way, maybe the creators of the show made a big error on Peter's abilities, or forgot to tell us about another possibility. :P