Samuel is, as you said, a good villian. I personally love his personality, and he sure is demented(possibly slightly more than Sylar xD). Yeah, I think the pressure of introducing more characters into the series was too much for the writers to put the focus back on the originals: Claire, Sylar, Peter, Mohinder, and Hiro. Though, Ando has my favorite power(yeah, I'm a sucker for energy manipulation
)
It's definitely way better than the last season of the series, honestly. As for the arc, I am curious about a few things,but I'm sure they'll be cleared up soonish. Most of all, I'm curious about that Seattle killer. And on a semi-relevant note, you have mad writing skills, and your story-telling is pretty wicked. Fanficion has never been my forte of writing, so my hate comes off to you *takes off invisible hat* :3