Has anyone considered that Peter might not actually be "reset?"
My theory is that the serum gave him the power of flight. We've seen that power types can run similarly in bloodlines. Nathan was different because his powers were fake. Now that Peter's powers are fake too, perhaps he was just gifted with the same power as his brother. So instead of being set up as a foil for Sylar, Peter is instead being set up as a foil for Nathan.
I think that's a pretty seriously large departure for the show. I doubt it.
The mythos of the series is that the hero serum gives you a power that is already encoded in your genes. You get what your latent dominant power is.
Peter's dominant power of absorption is already present; ergo, that's what he gets. Peter's immediate power of flight in the presence of Nathan is certainly consistent with that - though it does not rule out a redirection. What you suggest is possible I suppose. But...
I doubt that the writers will let go the possibility of nerfing Peter's powers with this reset though. They seem to go to great efforts to nerf them otherwise throughout the arc of the series.
It is possible, however, that they don't go that route. "We'll see".
The big surprise was leaving Hiro without his powers. We'll see how that works itself out. My guess, as stated earlier, is that there is some vestigial power left, but without Ando there, it's not enough to manifest. Alternatively, Vol IV is a quest for the return of Hiro's power. (Or both).
We do know that the formula has existed before and was used on at least Nathan and Nikki/Tracy/Barbara. Samples from that original formula may well be locked up in the Company's Vault in Odessa as that seems to be where they kept the other dangerous viral samples. That Vault was not disturbed by the fire outside NYC, so presumably it's still there - and would allow Hiro to get his full powers back at some point.