Season 2 was pretty bad mostly due to the writer's strike.

As far as Nathan's concerned, I don't think his dying and coming back was suppose to be a huge deal. I think the big shocker there was that Nathan was shot by Peter. In all honesty, I thought that with the cap and jacket, Peter looked a lot like Sylar.

I'm actually starting to enjoy the changing timelines too. It's not just "Yeah, I'll go back and change things" and then everything turns out just fine. They seem to be borrowing a page from Eureka in the sense that everytime someone goes back and tries to "make things right" things end up being a lot different then what they expected. I think it's getting the point across that as they try to make things better, they're actually making things worse. Didn't the X-Men cartoon actually explore this angle when they sent Bishop back in time to save the X-Men? And what What if? series did the same when someone tried to go back and kill Magneto.