Caitlin was left in the future, and they will never mention her again, according to Tim Kring. Due to the writers strike, they scrapped the idea of getting her back.She may not return to the series but there are many theories of time that could've happened to Caitlin.1, Positive Theory) It's possible that after Peter destroyed the Shandi Virus he altered the future and the 2008 he left her in changed around her into the real 2008 instead of the virus ridden one. Like in Back to the Future II when Marty and Doc left Jennifer and Einstein (the dog) in the alternate 1985, changed the past, and it changed around them. So she could be in New York somewhere but Peter just never met up with her due to his brother getting shot and the events of season 3.2, Negative Theory) When Peter destroyed the virus he may have destroyed the future he left her in and she is trapped in that future forever.
In a podcast Interview for Comic News Insider, Bryan Fuller the Co-Executive Producer and Writer for Heroes, confirmed that the character Sylar was written in the sense that he eats their brains to "digest" their DNA and adapt his own DNA to gain that power. It was never directly stated in the show as even the writers thought the statement of Sylar eating brains was silly and would spark Zombie discussions in the office.Sylar's initial super power seems to be an inate understanding of how things work (hence his watch repair profession). It's possible then that he opens up people's brains, like the backs of watches, so he can understand how they work. He even comments that he'd like to see how that power works when he captures Eden and attempts to take her power. In the one of the last episodes of Season One, Molly Walker tells Mohinder that he can't stop the boogeyman (Sylar) because "he looks into your soul and then eats your brain." It is easy for that statement by Molly to confuse people as they might assume that the 'boogeyman' is Maury Parkman, but it is important to remember that Molly was in the same house while Sylar killed her parents and used her father's brain to get his abilities. Maury was 'The Nightmare Man', Sylar is the 'boogeyman'It is anticipated that how Sylar absorbs the powers of others will be confirmed during the show's second season. Note that Chandra Suresh tells Sylar (through flashbacks) that the source of these latent powers comes from the soul, and the soul is kept within the brain, so it is logical to assume that Sylar gains his powers by taking in the souls of his victims by consuming their brains. There is also no evidence of brain tissue left when others find Sylar's victims, so any other explanation isn't as likely as simply "Sylar is eating their brains."You can download the MP3 file for the PodCast Interview here. The actual confirmation isn't stated until about forty minutes in to the Interview.In the recent promotions for Heroes Season 3, Clare is captured by Sylar, and says to him "are you going to eat my brain now?" to which he replys simply, "That's just disgusting." So it's possible he doesn't eat them. In the second episode of Season 3, "The Butterfly Effect", Sylar captures Claire Bennet and is seen softly touching her exposed brain after opening the top of her skull, prompting the afforementioned dialogue. Sylar reveals that his power to see the intricacies of working objects allows him to pinpoint the exact part of the human brain granting people their superpowers, which he then touches to absorb and copy their abilities. Up to this point, he had killed people simply to remove them from the picture, but lets Claire live stating "You're far too special, and I couldn't kill you if I wanted to. You can never die, Claire. And apparently, now neither can I."