I really keep hoping that they both wind up on the same side--the right side--but it looks to me like Nathan is going to his father's side within his mother camp and Sylar is doing the opposite. I really think it would be better for the growth of both characters if they both continued to redeem themselves for past mistakes and become great heroes. Nathan works best when he is working with Peter, not against him. And Sylar is now far more complex with his inner struggles. We have enough villains with Arthur, Tracey, Knox, Flint, and, in my opinion, Mohinder. Leave Sylar and Nathan on the right side.

Thoughts?

Don't you think that Nathan's hatred to his father outweighs anything at this point? I mean, in the very first episode, they showed Nathan doing the RIGHT thing in spite of having to take his father down..I'm not sure how that would have changed by this point.
You could also see Sylar changing into Gabriel as Elle was ripping away at him...essentially burning away the shell of Sylar and bringing out the Good (gabriel), that was buried beneath...

I think it's both pretty clear where their intentions are..Sylar may not be as clear as Nathan.

While I don't think that Nathan is a mole, the possibility is there. Remember: Tracy is intent on pushing him to Arthur's side. For all we know, Nathan is still on his mother/Peter's side. I mean for Christsake, Peter has been to this doomed future, that should be enough for Nathan at this point, but I think he is still a fence-sitter