Come up with an overall plan for the show. Each season will have a larger theme, as outlined below.
S2 -
The Death of the Heroes' Dreams of Normalcy. Early on, spend some time cleaning up after the mess of the finale. Then let the characters retreat to their respective corners. Do what they're doing now with Peter and Matt, namely that the heroes are trying to integrate their powers into their lives and/or ignore their powers.
Start to reveal the backstory of the heroes and how they got their powers (the Generations idea.) By the end of the season, the heroes should realize once and for all that they simply cannot live normal lives. This would also be a good place to broach the Villains idea - that having powers isn't something these people can easily control, and can lead to terrible things.
Kill Hiro and drop Ando from the plot.
Kill Nikki and forget the triplets thing.
Mohinder will never, ever, ever have superpowers. His role is to be the empathetic scientist who does what he can to help the heroes.
Peter should keep his swiss-army-knife absorption powers. They can limit him by having using the powers harm his health so that he doesn't dare use his powers without having an extremely good reason, and even then, presumably some powers are more costly than others. Flight is not too costly; mind-control is very costly. Calibrate the cost to the value of the power.
Forget about adding new characters willy-nilly; most of then have sucked. The good ones: Adam and Elle (who wouldn't be around long in any case since they couldn't keep Kristen Bell on TV).
All time-travel-using heroes learn early on that time travel generally does more harm than good. That alone should prevent its overuse.
Sylar can stay with the story throughout its whole run but should drop out of the storyline for long stretches so he doesn't wear out his welcome.
If they want to pull the Gabriel Petrelli plotline (and I'm not necessarily opposed), they need to start foreshadowing it in early S2 so it doesn't seem so pulled out of the writers' posteriors. Make some reference to a child born between Nathan and Peter in age that died before he ever came home from the hospital and nobody likes to discuss that tragedy.
Cast Peter Coyote as Arthur Petrelli and make him more interestingly sinister, the Godfather of mutants. He doesn't need to show up till S3.
S3 -
The Sh*t Hits the Fan. The end of S2 should have something truly catastrophic - half of NYC blows up for real or some such. This thwacks Nathan upside the head and he thinks he has to lock the heroes up for everyone's good. It's the Fugitives idea, but without character assasination for Nathan being the propelling factor. Nathan just needs a plausible motive.
The heroes are definitely public knowledge by now.
Revisit Micah, who has been living by his wits since his parents' death. Start to integrate him into the main cast.
Mohinder should develop a therapy (not a cure) for the heroes, which will suppress their powers as long as they take it. He experiments on Sylar with it and gets him to become "normal" for a while, until he inevitably decides he prefers being a fun maniac to dull normality and falls of the wagon.
Matt's attempts to use the therapy meet similar results - but that's because, as a cop, he can't stand the idea of not catching criminals by using his powers, particularly if he's put to some really tough test (rescuing a child who's been kidnapped by a pedophile ring or some such).
I don't dislike killing Nathan at the end of S3, or even the way they did it.
S4 -
We Have Met the Enemy and They Are Us. The upshot of S3 should be that the heroes cannot just run around loose, doing as they please, since bad things will inevitably happen. This splits them into two camps, the "tame" ones who decide the lesser of the evils is to work for the Company, and the "feral" ones who are still deluded enough to think they can live without restraints.
Matt and Mohinder will be tame, Peter and Micah will be feral. The others could go either way. Claire could be feral.
S5 -
Resolution. This should be the final season. Not sure what it should entail but there better be a kick-ass Peter vs Sylar showdown at the end.
In Season 1 you cared about the characters because you didn't know who would survive at the end of it. When they became popular and the networks demanded the same actors be used it became a foregone conclusion they'd be back. So all tension went away.
All TV shows have a regular cast that viewers expect to stick with the show, with major characters being killed off only rarely. So how do all those shows manage to hang onto their audience?
My outline does have a lot of major character deaths but that's because I'm trying to get rid of the useless ones, and while Nathan is far from useless, I think you gotta kill some good characters too, just to maintain credibility. But I'm not taking a chainsaw to the cast.
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Thanks. But Heroes really does have some good ideas - it's like Stargate, you see all these good ideas and then you gnash your teeth because the writers don't do anything interesting with them!