I think that is a really good idea, and you could start with badass Peter and Hiro (full powers) which is a bonus. At some point, it would have to be revealed how Peter got his scar and Hiro his goatee (equally interesting if you ask me). That way also, you could focus on a select group of Heroes, so Peter, Hiro, Claire (not that I want it, but it's inevitable, and I guess it might be bearable if she turned badass as well) Parkman (remember how he was a great villain in 5YG) and maybe a new character? Obviously, they'd keep Sylar as well, but personally I'm not too bothered.
Also get rid of unwanted baggage like Tracy, HRG etc. It would be something completely different, maybe a bit of a risk, but if it payed off that would be awesome. If they could get that right, I think it would be an awesome idea.
Anyway, what do you guys think?