1) In a better TV show, the writing could have convinced me that Sylar had been reformed, but they didn't show me anything to make me think that. Besides, I believe that the official count says that this is the 37th time that Sylar has switched from good to bad or vice versa.

2) If Claire weren't such a dim-witted brat, once she found out that Jacob could show her her father's memories, she would have immediately asked to see the memories of him shooting up the carnival, not wait until she saw all that other stuff. Though it was good to get his backstory, that was an annoying way to do it.

3) This bugged me most of all. Noah's partner (can't remember her character name - she's Kate from Angel), despite being shot in the shoulder and with no super powers, she was able to somehow escape from the replicating dude? Uh, sure. They can't expect us to believe that, and to believe that that dude has any chance in hell in even slowing down Peter and Sylar. That's going to be a complete joke. Not only that, but it's how they told us she got away. The replicating guy comes on-screen and basically says "uh, she got away." What he's really saying is "we need to forward the plot but don't have to enough time to show a regular, injured woman escaping from someone who's impossible to escape from, because we have about 37 different plotlines going on."