My general thought is that Peter's powers cannot return full force until he needs to be a match for Sylar's powers, otherwise he's too powerful. He seemed to expect Nathan to betray him so maybe (??) he's learning, but I doubt it. Parkman is another who just doesn't seem to live up to his potential. Is Daphne dead or just in custody? I don't remember seeing her after she was shot. The whole painting the future thing also bugs me since it's supposedly malleable. However, everything that's been painted has come to pass (unlike futures which may be traveled to via Hiro's former ability), this just seems like an overused crutch to make up for lack of an intelligent hero (while the main villains seems to be plenty smart and don't need such a tool).
I was wondering how the heck Claire called her father while in the same store with him and he couldn't hear her... I'm waiting for Micah to show up as he would be especially useful in a war like this.
Why did Tracy kill that man? That made no sense at all.
Seasons 2 & 3 did pretty much suck (3 was mostly good but the ending just didn't work for me).
Oh yeah, where's the girl Parkman and Suresh were taking care of?? She would be amazingly useful here.