Spoiler
1. I understand that the future is malleable, but they've sure gone out of their way to show that the future from which "goth Peter" came can't happen (no happy familiy life for Parkman, for instance).
2. If the heroes have to go "off the grid" to avoid capture, how did Hiro and Ando get to India? Hiro couldn't take them, and surely their names are in a DNF database.
3. So Peter can still duplicate powers, but now only one at a time. Somehow I think that makes him a better character.
4. Sylar as surrogate father to the "microwave kid" just doesn't make sense, especially given Sylar's comment in the diner that "emotions cloud the judgment" (maybe he's channeling his Spock character).