I highly doubt that will happen honestly. However, I've been known to be wrong before, I just think that in that case Pete would have had to absorb Sylar's Intuitive Aptitude (as weak a suggestion, at least partially, for Sylar's behavior) to get Sylar's "evilness". Given Peter's previous experience with the ability, I doubt he would have chose that. As far as potentially absorbing Sylar's consciousness, I doubt that as well, seeing how it took a powerful Telepath to virtually rip it from his body (albeit unintentionally).
Sylar wanted his body back, so I truly think that he is sitting inside "Nathan's body" more than likely waiting for the right time to strike OR he hasn't fully manifested himself there yet, as it took him at least a few weeks to show up clanking around Parkman's skull. Despite all his power though, Sylar's no idiot. He's shown to be resourceful not just through his ability, but through his manipulation of people/situations. Either way, he's most likely to show up at a time where he can do the most damage.