Temis the Vorta: Do you think it would be better to kill off Nathan by the end of Season 3 of your Five Years Gone vision, with Sylar assuming Nathan's form out of survival and then during Season 4, Sylar becomes seduced by political power and becomes bent on becoming President to gain more of that power?
I think Nathan should be Nathan when he wins the Presidency. I don't see Sylar ever having the savvy and discipline to pull of a successful Presidential run, regardless of who he looks like. He'd be under far too much scrutiny to be able to maintain the facade impeccably. And Sylar is a scavenger: he'd let Nathan do the work and then grab the glory, maybe right before the Inaguration.
When "Nathan" enters the Oval Office, the audience should be uncertain just who they are looking at. They realize the truth only when the new Prez sets something on his desk: a snow globe that says Souvenir of Oregon.
(I like the idea that the snow globe is Mount St Helens spewing "ash" instead of snow. I don't even know if they make such a thing but it would be a nice joke.

)
And maybe Peter and Elle could have a passionate affair
I always thought Peter was
scared of Elle. I can't see that relationship working out at all.
Why not just kill Sylar off in the S1 finale and have there be a new villain for each season?
If they can come up with a good villain for each season, sure. But look at their track record:
Sylar - they got a terrific actor to play a poorly written villain.
Adam - they got a terrific actor to play a poorly written villain.
Arthur - they miscast the role, which was poorly written anyway.
Elle - they got a terrific actor to play an inconsistently but not terribly written villain but they couldn't hang onto the actor.
Danko - they got a terrific actor to play a an okay but too cliched villain.
Samuel - they got a terrific actor to play a poorly written villain.
This pattern doesn't fill me with a whole lot of confidence.

Why bother killing a character if the next one is going to suck just as much? Killing a character means you lose the actor but keep the writers. They need to do the reverse.