I should dig up the old posts I saved on this topic, but to be brief:
1.
Every major character on the show needs their own arc. Where are they going? How are they evolving? When they reach the end of their arc, they die or leave the show. If you can't figure out an arc for them, they are relegated to minor status or killed immediately.
Details like "should Peter ever be depowered" or decisions about what his powers are, and the logic behind them, should be determined by his character arc. Anything that serves the arc and can be integrated well into the overall story is a good potential story direction.
2.
Decide who Sylar is and stick to it. Is he a normal guy made crazy by his powers or a crazy guy made worse by his powers? Both approaches have pro's and con's. Figure out which is the lesser evil and go with it.
3.
Accept that there are unkillable fan favorites and work within that constraint. Sylar, Hiro and Claire are all a nuisance to write for, but that's why you get paid the big bucks to write for network TV.
4.
The theme of the show is: can people who gain the powers of gods ever learn to use them responsibly? The theme is not: people discover they have powers. That's not a story, that's the beginning of a story.
5.
Avoid crappy writing such as stupid characters, incoherent plots, bad dialogue, et al. Professional writers shouldn't even need to be told such things.
have at least one character running around using their powers for good as vigilante, have at least one character out themselves and use their powers to be a showbiz sensation and one character out themselves by being a complete fruit-cake villain out for WORLD DOMINATION!!!!!!!! BWAHAHAHAHAHAHAHAHAHAHAHAHA!!!!!!!
Great ideas! You're on the writing staff.
Another thing that would happen: at least one character would have a possibly looney religious interpretation of his/her powers (possibly even imagining they are the Second Coming) and behave accordingly. They pussyfooted around with this a little for Nathan, but Nathan isn't the right character for this plotline. Not sure who is, maybe a new character.