My understanding is that Nathan's actor is signed for season two -- which leads me to believe he'll be alive. Granted, with the time travel and flashbacks and flashforwards, nothing is a given...
Mohinder adopting Molly would be adorable! As long as she and Micah can still be my miniOTP.
I'm really intrigued by what S2 will bring. My roommate read a casting spoiler that there is a new character who will somehow be involved with the roaches we've seen at various "death" scenes (including Sylar's in the finale).