What they needed to do with
Villains, and rest assured, this is just a partial list:
1. Stick with the notion that to use time travel effectively requires also having the ability to know what to change - Sylar's "seeing" ability - and without that ability, time travel is pointless. This will stop the time travelers from embarking on pointless stories. It would be nicely ironic for that ability to be part of the mix, but rarely used, because it's not actually all that useful.
2. Establish that the S1 finale, in which half of NYC was not blown up, was just a temporary fix and in fact set in motion something far worse. (This may actually have happened - is the planet still due to crack in two? I can't recall if this plotline is still in effect or if it's just one of the many that have been dropped.)
3. Establish that Peter has to obtain Sylar's "seeing" ability to stop the coming catastrophe. Don't just have him get the power and then lose it before this plotline goes anywhere! Carry it through to some impactful conclusion, such as, he saves the world but the insanity drives Peter to do something truly awful such as killing a major character (and for a better reason than that the character is useless and should die.)
Claire obviously would have the most impact but that may be too much for Peter - don't want to drive him over the edge. The best option is that he kills Ando - he'll definitely feel bad about killing a sweet guy like that, and it will mean something for the audience - and that will have the added advantage of giving Hiro a chance for a character direction, namely does he forgive Peter for being insane at the time (after all, he was just doing something loopy in order to save the world - Hiro should understand that!) or does he go all Badass Hiro and pick up a samurai sword?
Or come up with something else, but it must be impactful - it changes Peter and it changes the plotline.
4. Cast Peter Coyote as Arthur Petrelli. The guy they got was awful. Peter Coyote is one of those fun actors who can make something out of a role even when it sucks. Of course, Arthur should not be written so that he sucks. He should be a charming megalomaniac who has been used to extreme power for so long that he's convinced of his own right to obtain as much power as possible.
After decades of stealing powers, he's pretty much got them all. His main concern is to re-establish his power and pass his legacy on to whichever of his three sons is the most deserving.
Gabriel is not Angela's son - I'd keep Virginia as his mom. After Nathan's birth, and testing determined that he just would have lame-ass flying power (forget the notion of artificial powers, that's dopey and unnecessary), Arthur figured that Angela might not be a good genetic match for producing the successor he had in mind. So he committed bigamy in order to give himself more options. If he had the splitting power, that would be simple. He might have married more women than just Angela and Virginia. That would be a good element to leave open and use later, or not.
I'm not sure whether Arthur should also be the watchmaker. Maybe they could establish that watchmaking is his hobby. If he were split in two, he could be a lawyer named Petrelli and a watchmaker named Grey very easily.
He stays with Virginia till Gabriel is an adolescent and then bails, secure knowing he has at least one son with the "right" kind of power. In the meantime, Angela has given him another with another flavor of the "right" kind of power. So Arthur has two successors who he plans to pit against each other.
Of course the difficulty is, 1) Nathan is the most natural leader among all his sons, 2) Peter is unlikely to fight anyone for power, and 3) Gabriel would jump at the chance to run his own mutant empire but he's too unstable. Cutting open your employees' heads is not an effective managerial style. As stable as Gabriel would like to be, in order to make daddy happy and inherit the kingdom, he simply cannot be stable long-term.
There won't be any ping-pong between Gabe being good and evil; the struggle will be internal, between his need for power and his need to kill. Power and killing used to be the same side of the coin for him, and now they're opposite sides - he's his own worst enemy. That's how you solve the Sylar problem (for a while).
I don't know what story you create from all these elements, but add in the fact that Peter will no longer be able to sit in judgment of Gabriel's psychotic behavior quite so much anymore, and Nathan will stop dithering and directly battle Arthur to keep either of his unstable brothers from obtaining power (and to protect Peter, who is in bad shape after killing Ando or whatever), and the battle between all five members of the Petrelli family could be fascinating. All the material was there, the writers just didn't come close to putting it together correctly.
5. Forget about Elle teaching Sylar how to get powers without cutting heads open. Sylar is Mr. Cutting Heads Open. Keep it that way.
6. If Sylar is battling Nathan for power and Nathan is protecting Peter and Hiro wants to kill Peter, that might make Sylar and Hiro natural allies. Hmm, that has some fun potential...
Okay that's enough for now. I could keep going, trust me.
Villains really gave me a headache trying to keep up with what they were doing. If they hadn't backtracked and left Sylar as a Petrelli, and left him somewhat calmed-down, and left him and Elle together, then perhaps the show might have started to get somewhere.
