Season 1:
Cut some of the fluff from Peter's story and fill in D.L.'s plotline (see deleted scenes from episode 1 to make them more relevant).
Add a few more skirmishes to the final fight, add a more dynamic 'teaming up against Sylar' facet to it. Bring out that Sylar came to stop Peter from blowing up. Let D.L. Sacrifice himself to hold Sylar still so that Hiro could stab him.
That's all. Everything else was awesome.
Season 2
- Give Sylar Peter's whole plotline, from amnesia to kaitlin, to painting a gallery of a diseased dead future battling his forgotten dark side to teaming up with Adam and almost releasing the virus. Peter fears his own powers because he's responsible for his brother's death.
- Give Peter and Monica the preferably-dead-despite-that-they-were-great-characters Nathan and Matt's finding the 12 storyline. Make Paula Hawkins one (where Peter meets Monica) and send them on a worldwide tour finding out all this crazy stuff about the past, the most looming of which is the virus. Do not kill them all off in one bit of dialogue. Make the series of 8 paintings the deaths of the remaining 12, including Angela, Bob, Maury, Hawkins, and Adam.
- Let Hiro's journey in the past teach him sword fighting skills and warrior's bravery, then send him into various time periods related to other characters in Lost-flashback/flashforwards style. He gets a birds eye view of the Generations effect, even meets our generation's kids and Future Future Hiro.
- Claire is discovered by the Company, and becomes an operative, and quickly, a good one, and is teamed with her father, HRG. Morally grey and hard parenting lessons ensue.
- With the cleared space, Maya and Alejandro's journey brings them into contact with
- Give Candice (and Adrian Pasdar) something to do, with a subplot where Candice acts as Senator Petrelli after real Nathan's death and slowly, Candice gets enveloped in Nathan's life. Becomes nemesis for Peter.
- Make Mohinder, Nikki, Micah and Molly a very odd family unit, trying to live normal lives, and keeping large secrets from each other which eventually break out. Give Mo and Nikki a tragically failed romance subplot. Mohinder gets stuck in the company and paired with Elle, but Nikki Micah and Molly are the ones he betrays, not HRG. Between the two of them, they tell powerful stories about family, which again tie into Generations, which is about family. Jessica would be Nikki's sister with the power of body-jumping (explaining the tattoo).
- Do the whole 1975 episode as it should have been.
- Make the Haitian a well-rounded character, even giving him a name to reveal at the end of the season.
- Will likely end in a battle between the 12 and the current generation, where the old heads show just how devastating their apparently benign powers can be.
Season 3
- Finish off the Virus storyline proper, since the writer's strike would stop the second half... insert a time gap in the storyline to reflect the time gap for the viewers...
- Use Maya to combat/cure the virus, as originally planned.
- Second half, Villains, make them utter badasses, destroying the Company almost completely by episodes 1 and 2. Use them as metaphors for every type of crime conceivable. Let them go unerase Sylar's memory and dig up Adam. Let each "Hero" battle with their conscience, but only let one fall, and let it be an important and unprecedented fall, like Claire or Mohinder, and let it make sense.
- Because of the nature of the Heroes movement, each villain would have ties to various characters, old and new in shocking and often dark ways.
Clearly, I've given this too much thought. I have a spreadsheet around here with episodes as columns and characters as rows as far as what I would change.