I feel much the same way you do. Season one felt really uneven, but there were relationships I did really care about, pretty much the same ones you've named. Petrellis. Claire and her dad. Claire's relationship to the Petrellis. Hiro and Ando. The dynamic between Mohinder and Sylar. Instead of building on that, they spit up all those relationships for most of the season. They introduced way too many new characters when the story couldn't really support all the characters from the first season. The pace was plodding at first and then everything just kind of whipped by.

Today, I've felt more convinced that Nathan won't be dead, but in some ways, it would be easier if he were. Then I could just stop watching without any regret.