I loved the finale and I think the Nathan/Sylar twist is one of the best things done on the show.
I preferred season 3 to season 1. Season 3 was a lot more focused on a main plot thread. Season 2 actually had an arc with the Shanti virus, but Exodus never came to fruition and had to be made into Villains (Sylar getting his powers back basically became the end of that arc). Season 2 was a victim of the writer's strike and certainly is overall the weakest season for it (that and too much time in feudal Japan). The focus going to the Bennets, Petrellis and Sylar was a good thing, IMO. They are ultimately the core that can't change. Niki was always the weak link in season 1, because her plot importance was basically only with Linderman and marginally with Nathan. Tracy is a lot more connected to the plot now. Micah improved when he got rid of the dead weight of his family and became Rebel. He was a bigger part of the plot of season 3 than Niki, D.L. and Micah ever were in season 1!
And I don't expect Sylar or Nathan to be going anywhere just yet. Or even at the end of the season.
Sylar getting Claire's ability and wanting to have Nathan's life has been in play since the end of season 1. This IS the show's arc. Notice how every possible future has Sylar taking over the lives of the Petrellis or Bennets and becoming a better them than them? In one future, Sylar has become President Nathan, and in the other, Gabriel has become Holly Homemaker (or actually, he's become Noah--all he wants is to "protect [his] family") in the Bennet house and has Mr. Muggles and a son named Noah. Gabriel's story is deeply rooted in his obsessions with Noah, Nathan and Claire.
It makes the moment with Sylar fixing Danko's father's Soviet watch even more poignant. "That's the only one that was ever truly mine." He wants love and acceptance by becoming special--a result of his adoptive mother, not just by planning to become the only one left along with Claire--whom he can't kill and wants to keep around so he doesn't become his father, but by having what makes the Bennets and Petrellis special with a side-dish of revenge on Noah. Sylar going from a seemingly clear-cut villain (unfortunately, some viewers who like straightforward good vs. evil don't like that he didn't remain 2-dimensional) into a sort of a tragic figure of identity has been happening since season 1.
Sylar is just another face Gabriel put on to try to become special. Gabriel doesn't have any tangible ability that is his own and thus tries out other people's lives and abilities, trying to find what makes him special. It's why he goes berserk when he can't even keep his own identity straight with the shape-shifter. Being mixed up with Nathan, with Nathan's life and Nathan's memories is part of this identity crisis storyline--but this time, even though this is what he always wanted, it's forced on him. It gives context to "I want my body back." He gets what he wanted, but probably won't be happy about getting it in this way. It's just another example of Gabriel trying to become special with some else's identity and never being satisfied with it because it's not *him*.
And the "ordinary people" thing was never sustainable; it's something all the characters try for, but will never achieve again. That has been used in many franchises where characters realize that they are different from other people. That move from 'ordinary and in the world' to 'extraordinary and outside of it' comes with the territory.
As far as Claire's blood... Nathan had his throat cut and had already bled out. A transfusion can't get in your bloodstream if your neck is gaping. Also, apparently Noah wasn't completely dead, whereas Nathan entirely was. It's a matter of Claire's blood being able to heal the almost-dead, not the completely-dead. That's the official word, anyway.
Enough with the bashing.
