Obviously, a major problem with Sylar being Nathan is that, well, he's Sylar.
That comes with some inherent abilities, as the preview showed.

Too bad we don't have a baby who can turn powers off...

Now, before it's said, I might as well address the fact that we do have a loving father who could guide Baby Matt on how to turn off the right powers.

Or just get the Haitian to disable him temporarily and then chop him up into little bitty pieces. That way, it'd be guaranteed that the kill spot would be well and truly hit, regardless of where he decides to move it to.