More specifically, what's going on with his ability to regenerate?
In season 1, Claire's ability was a big deal for Peter. Sylar shanked him in the back of the head with some glass and he was able to get back up once the offending object was removed. He exploded with the force of a nuclear warhead and survived thanks to the fact that he had met Claire and copied her ability to regenerate.
He even held onto it through season 2 after he had lost all his memories, or perhaps that was just Adam's ability. Either way, he regenerated when Victoria shot him and he got right back up.
Now, however, he seems to have lost the ability completely. Last week, when Future Claire shot Future Peter a few times in the chest, he was declared dead without a second thought. When Future Claire was torturing Peter with the scalpel that same episode, his cuts didn't heal and were still there in the next episode. If I'm not mistaken, The Haitian had left the room during the scalpel scene, and Peter knocked him out when he ran away from Future Claire after Future Peter was shot. When Sylar slammed him ito the glass in the episode yesterday, he went down like a bag of hammers.
Did I miss something in the last few episodes that would explain this, or do the writers just think we're all stupid and won't notice this?