I actually agree when it comes to Claire. Since I saw they first said Claire is dead I knew even if they cannot get the actress back, they'll use her for a plot that reveals her alive and in hiding.
Since you are a Sylar fan I thought I'd toss in another theory that has lost some weight since the 3rd episode but still a possibility. When I first saw the male character who brought in Molly Walker, I noticed something specific about his power. It's not just using any generic sound effect, it used the same one as Sylar's powers.
What if he isn't just any new character, but Sylar using his shape-shifting abilities? Yes the last we saw he was trying out the whole being 'good' thing, however; in the last two seasons Sylar was shown time and time again being manipulated by others. First he was convinced that he was the lost son of the Petrelli's, then after the mind wipe slowly faded he was taken in by the carnival. I wouldn't put it past the writing to say that he's was convinced that what the company is now doing is good for people like himself, and his shape-shifting is to hide his true identity.