ok here's my long shot theory for Mr bad evil guy number two.
Dr Suresh said he thought he found Patient Zero, Patient Zero would be the first person with powers. (though, are powers contagious? they seem to have dropped a few hints now indicating that they may be. but more on that later) He had a name nothing else really. Most of those names came from a DNA repository. We know that Sylar clearly isn't Patient Zero, if fact he is a member of the second generation (assuming that there haven't been heroes since the 1600s) Linderman, Angela, Simone's Mom, possibly Pappa Petrelli (though I still have my doubts) and possibly Nakamura senior make up the first generation. If there was a Patient Zero, then obviously he would be a member of this generation. And he would probably be quite powerful. So, here's the question, do we know the name of Sylar's father? Is it possible that Sylar's name is actually Gabriel Gray Jr.? Could Suresh have been looking for Gabriel Gray Sr. and came across his son by mistake?
Back to the powers, In the comics on NBCs home page, we see in Six Months ago, some people who at the time didn't have powers, running into people who did. Later, they developed powers themselves. Also in the comic, Linderman had powers, but Petrelli did not, but later it seems that Petrelli, at least according to Linderman, developed powers as well. So did he catch them? does using your powers on someone give them powers as well? if not then what was all that about?
Another theory of course is that Papa Petrelli is alive and well after faking his death, and is the big bad guy, though I doubt it.
Sulu is another guess, it would seem that at one time he was with Linderman, but now, he is working against him.
Or it's just someone we haven't met, Maybe the Samurai we saw at the start of Volume 2.