Honestly, I don't think so. I think both Peter and Gabriel were supposed to be done after season 1. An amnesiatic Gabriel with a dark side isn't interesting to me. And if they wanted to do that, why wait until season 4 to do it? I wasn't really interested in seeing a redeemed Sylar. He was much more interesting as a power hungry killer that came about because of extreme emotional sheltering.
I will give Heroes props for finally finding an interesting way for Sylar to become good in Season 4. (It was better then what they did in 3 anyways). But I think it's fairly clear that Sylar was supposed to be done after season 1. The character had no where left to go. If they had a plan for his character post season 1, I really doubt his story lines would have been so incredibly muddled as they were. They had no clear vision.
And I think a Sylar who chooses to be evil as opposed to being driven by a "hunger" was a much, MUCH more interesting character. Not to mention it makes more sense. Sure, Sylar is driven by an internal hunger...but that only explains why he kills supers, not why he wanted to blow up New York.
Sylar was a great villain, but bringing him back was one of their big problems.
Let me clarify: I don't like season 2-4. There are scant few things I enjoyed, and I feel they utterly destroyed the mythos by retconning things that made the series great and turning into the Sylar Show. I'm not a Sylar fan, but I find the Gabriel Grey character interesting and useful.
To answer your question: why they waited until Season 4 to do it? That's when Kring got some control back. When they originally wanted to do it, season 2, they were compelled by executives who thought the knew better to keep Nathan and Matt on and front and center, and that Sylar had to stay Sylar. That meant giving them the Generations storyline that was a natural fit for Peter (former show center) and a new character (new show center... Monica?). This meant that Peter had to go somewhere, so they gave him Gabriel's amnesiatic kaitlin-loving unknown dark side, Adam-lackey storyline, and they tacked on a brand new Sylar storyline to Maya and Alejandro. No matter how uninteresting you find amensiatic Sylar with a dark side, amensiatic Peter with a darkside is even less interesting, especially before 3 years of Sylar being shoved down our throats.
My point: keeping Matt and Nathan and Sylar evil caused the problems. Keeping Peter and Gabriel was set up in season 1.
On Peter
If you remember back then, Peter was pretty impotent, and he was an empath, not an overpowered power copier. To use powers he had to reflect on those individuals, to remember how he felt about them, how they felt. And he wasn't good at it yet, not at all. In a traditional 3-act superhero movie, they call this the Origin part. He hadn't faced any great challenge, and certainly had attained any victory over the master villain (his father, in his case, possibly Uluru), he was just learning what his power was, and experiencing the tragedy (being responsible for the death of his brother) that would galvanize him into action. With a guilt for his brother's death and a vendetta against his mother, Peter was well poised to be in a bar drinking himself into a stupor, if possible, arguing with Angela and investigating the Generations storyline. In short, he was poised to grow as a character, based on Season 1. I'm not sure why you thought that the character who had just killed his brother was supposed to be done. That was not clear to me at all.
On Gabriel
This character had less potential, but remember, before the extreme meddling and overhaul of Kring's vision, Sylar saw all his kills flash before his mind. Something happened to him when he got stabbed that involved his mind and his stolen powers. Did he lose them? Forget them? In one way or another, Hiro killed "Sylar." But, as we saw, his body was taken, was it alive? Was it for experimentation? Did he drag himself? Did someone else? You say Sylar should have stayed dead... but no one said he was dead in the first place.
Before S2 was torn asunder into suckitude, something of Sylar was supposed to survive. Since, as was clear, the Sylar storyline was done, my bet is it was Gabriel Gray. One thing I would have loved to play with is: "If we remove Sylar from Gabriel, will he turn into Sylar again, or is Sylar the product of a specific set of circumstances (ie PaPa Suresh)."
I think Sylar should have been done after the first season.
Nothing they did with Sylar's character after season 1 was interesting. He was absolutely amazing as a heartless serial killer with a thirst for powers, and absolutely sickening as a man searching for his purpose.
But in the same veil, nothing they did with Peter's character after season 1 was interesting.
He made an absolutely brilliant naive optimistic hero who had absolute faith in his destiny and the people around him. He made a terrible confused guy with a trouble past contemplating his darker sides and getting manipulated and tricked by everyone.
You know, now I think about it, most of the characters fit this trend.
That's because they didn't give those characters their original storylines from the five year plan, not because they were done with the characters.
Was Gabriel Gray, with Suresh on in his watch shop or at his mother's house *sickening* as a man searching for his purpose. That's where the potential in the Sylar character was, and I believe the original plan was to tap that before someone decided that Sylar had to stay Sylar.
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