My theory on a battle between Nathan and Sylar is this: Sylar hates himself. Sylar has a tendency to reinvent himself at the drop of a hat. He was so upset when he was shapeshifting into someone he thought of as a nobody - he was afraid of losing himself to Agent Nonentity. But, when the idea occurred to him to take over being *Nathan* - well, he was excited, to say the least. The battle may very well be Sylar coming to terms with whether he would rather be Sylar - and all the self loathing that comes with that, or commit to being Nathan, who has a family, friends, and the respect of complete strangers, just by virtue of being who he is.