I guess I'm seeing it in the opposite way. I'm seeing it as all the Heroes/Villains are somehow inextricably linked together. These people didn't just suddenly pop into existence the first time we saw them. Claire's mom worked for The Company, which makes perfect sense since I believe Noah knew about her during Season 1. She's never mentioned working for the company to Claire though, as far as I can remember. And we now know that Nathan's dad was involved in the accident that crippled Nathan's wife.

Most of the people have been brought together by the actions of The Company. That makes perfect sense since The Company has been hunting down and finding these people for a while.

Personally, it seems to me that they're trying to explain how everyone got into position in Season 1 and why Arthur only appeared to be dead but actually survived the poisoning. I'm looking forward to seeing if Peter gets his powers back and what happens with Sylar now. Everyone's powers are either gained through their family line (Patrelli's) or were given to them by that doctor. Who's powers are natural and who's were given to them remains to be seen (we only know of two so far).