My kids came up with an interesting suspect: Sylar. I'm still backing HRG as the shooter, but the young ones made some sense after re-watching the Saeson 1 episode Five Years Gone. In that one, Peter accuses Sylar of killing his brother. At the time the episode first aired, I just assumed Sylar killed Nathan the way he killed all his victims. But as Hiro's experience with the waitress in Season 1 showed, the fates of the characters seem predetermined regardless of what happens to change their current path.
So it would follow that Sylar is destined to kill Nathan in some way, if not by cutting off the top of his head then by shooting him. My problem with the theory is how Sylar got from New York to Odessa so fast.
I guess we'll have to wait until the fall to find out.

