Nathan is dead?

From my understanding I know Peter can only hold one power at a time, and the power he took from Sylar is shapeshifting.


He did say "I bet you weren't expecting me to take that one."

Frankly, Tim Kring is playing with his viewers. Remember that since time is a variable is his series he can always go back and make the required changes to suit his requirements or even rectify any mistakes or things that were not logical. The series has many unanswered questions and sometimes even the viewers tend to forget most of the things that happen in the previous seasons.
The next season must have some really solid storyline if he likes the series to be as interesting as it was in the beginning.
I hope the makers don't rush but take sufficient time to come up with some good thrilling episodes.
And lastly, I strongly believe that Nathan will be brought back in some or the other way..

Claire's blood can't resurrect the dead and since she wasn't in the room when Nathan was dead, her blood would be useless.

We clearly can see that Nathan died. Only Nathan's conciseness was transferred into Sylar. I think in the next season, Sylar will start to remember his life. Nathan conciseness will try to suppress him but finally Sylar will win. All hell will break out again. The chances to see Nathan to come back alive is very low but that is only my opinion.