Hmm, I didn't think about the time-travel stuff in depth. So by destroying the virus, Peter has just blinked his girlfriend out of existence? Or perhaps she lives in an alternate reality? Gah, it's probably best left to see how it pans out.
I wish they had shown more of a Hiro/Kensei struggle, but that really is a very frightning way to end that storyline, though I don't know why, but it borders almost on dark humor(probably cause Hiro's music theme is light-hearted, and it played before the revalation). So we know Adam can survive indefinitely under most circumstances, but can he survive in an enviroment completely devoid of food/air/water? I think Hiro may have left him to a fate far worse than being shot through the head, or chopping his head off, cause Adam will probably die, but it'll be a very slow, and painful death(much like the Sarlacc Pit).
Micah's cousin storyline, still dumb in my opinion. Could they not have come up with a better way to leave Nikki in an "unknown" situation? That's really my only complaint on the ending, everything else was solid.
And why did he waste so much time prying the vault door open when he could have just walked through it?

Good point! But I guess they had to make everything more dramatic.
Peter has so much wasted potential. He's the most powerful character, yet Sylar almost successfully beat him at least twice in Season 1, and he was a tool this season, barely thinking for himself.