Before they pussied out, Season 2 was supposed to have a totally different cast, so I'm assuming Nathan and Peter were going to die. And yeah, Nathan got saved by magic blood in Season 2, magic blood in Season 3, and now in Season 4 he died, but lives on through Sylar because of fat cop. I guess not resorting to magic blood is an improvement. The show doesn't really bother having consistent rules with how things work.
A big part of Season 3 focused on removing powers being some huge obstacle while Sylar got his powers removed in Season 2. Sylar's first power was knowing how things work and there was some hunger associated with it, but in Season 2 when he lost his powers he still went around being an evil dick. When he got his powers back, he had telekinesis when that wasn't his own power.
Heroes sucks