Just to keep this next season from being the mess that season 2 was:
Limits: There needs to be some clearly defined limits on the powers. As it currently stands, Peter Petrelli and Sylar are at this point GODS; as both season finales displayed, no other character has a chance against either of them at this point, and they are both reaching a number of powers that are eclipsing the Silver Age Superman. Furthermore, the whole "Ressurrection via the blood of Claire or any other super-regenerative being" should have some kind of major drawbacks, otherwise it becomes a deus-ex-machina that will allow just about anyone to return from the dead (Isaac Mendez, anyone?).
Originality: Hey, I love plot ideas and story elements from comic books being incorporated into the show as much as the next comic nerd, but there are plenty of other ideas you can use, even some of your own! Keep that in mind.
Answers: What exactly is the purpose of the secret cabal? How long have they existed? What have they done? How long have their been superpeople and why haven't we heard more of them? What the hell was the point of ANYONE keeping Sylar alive? (My theory: They wanted him as a deterrent against Peter in case he ever went out of control). Why did they feel they should shoot Nathan when they had a host of other, less lethal, methods?
Heroics: Outside of Hiro, not one of these characters does anything for selfless reasons. Peter is usually only helpful when he has a prophecy to prevent or his love interest is jeopordized; not exactly heroic ends. Nathan is more heroic in my opinion.
Things we don't need any more of: Emo Peter. Putting Peter's girlfriend in peril/killing her. "A DARK FUTURE I MUST STOP!" Emo Claire. Jeph Loeb (Trust me on this one).