Everything Nathan has ever tried to do, hes messed up. Hes easily manipulated, easily bribed, and makes horrible judgement calls. Where the heroes are today is because of him. Their secret is out because he went off the deep end.
Now look at this another way. Sylar is technically Nathan now and will be making decisions for our heroes again. However, now that Sythan has the ability to see how things work, he has gained the know how to make proper decisions. He now lacks that impulse that drove us to where we are today - ignorance.
I think "Redemption" is Nathan realizing that something is wrong, but still doing the right thing. Using Sylars abilities for good instead of evil and fixing all that has gone wrong. There will be struggles along the way with both personalities coming out at certain times, but I think in the end Nathan's strengths will overcome Sylar and we will see someone sacrificing everything to save the world.
I think Sylar/Nathan is going to turn out to be the hero, and will be killed off at the end of the season - FINALLY.
