There are LOTS of unawnsered questions so far.... Will they be awnsered soon I wonder, or even at all? Let's review some of them... If I missed one, post it....
In the first Episode's, there was a little girl that Matt found hiding, after her parents were slaughtered by Syler. She did manage to escape Syler, when Matt saved her again at the FBI headquarters. So where is she now? She must have abilities right?
Everything I say is my own theory, based on no spoilers.
I think she is still in a safe location. There is a theory where people believe the daughter may simply have a power amplification ability, which is why Matt heard her from such a long distance. But I don't believe that theory.
Which side is Natethen Peterelli on?
IMO, Hiro is the ultimate lithmus test of good vs. Evil. If you like Hiro you're good. If you can talk to Hiro civily at least, then you're grey, but able to be good. If you don't like Hiro, you're evil. Hiro's father is a strange one to consider, since he obvious has the duty of being his father, but he's annoyed at Hiro. So IMO Hiro's father is grey.
So what about Nathan? He gave Hiro a ride, and he seems fairly nice to Hiro but not too friendly, so I think he's gray, but can be a good guy at any time. He likes power, which is why he is working with Linderman so he can be a US Congressman. Nathan is on Nathan's side. He may feel obligated to Linderman, but even Nathan wants to use Linderman for his own ends.
Is Hiro's dad above everyone in the hierarchy of this new company?
If he's not above
everyone, then he's pretty high up. From what we can see so far, Bennet's use of Japanese;
1) To speak to Kaito Nakamura.
2) To confuse Matt Parkman.
Maybe we'll find more reasons in the future, but it seems to me that Kaito Nakamura is such a big name in the Company, his underlings learn Japanese just to talk to him. He wont even bother with translators.
If Bennet really wanted to learn a language that would confuse a mindreader, he could have chosen a dead language to do that (Aramaic, etc.)
Is the company just there for taging the heroes like animals?
They want to use the evolved humans to rule the world, probably. They also do experiments on them, perhaps to isolate the genes and mechanisms for superpowers, in the hopes of infusing these isolated materials into non-evolved humans' genetic structures. Thus, they could pick and choose exactly which powers their agents have.
Remember how Bennet was marvelling about how Sylar had taken on several powers? That was probably a major Eureeka moment for the Company, unless they've dealt with empaths like Peterbefore. We know that Claude had met at least one empath before, but we don't know if Claude met empath(s) before or after he left the Company.
So these little details will go a long way in us figuring out exactly what's going on.