As far as Nikki and Hiro, getting the drop on Sylar, that's very easily explained and fairly obvious with his character, especially in Nikki's case.
If Sylar has one key flaw, it's that he's disgustingly arrogant and proud. That pride often puts him in an advantageous and intimidating position, but it absolutely fucked him there. Think of it this way, you're standing here in all your power and some wafish looking blonde woman walks up to you. Do you take her seriously if you're Sylar? He likes to toy with his victims. His thought process was probably along the lines of:
"WTF bitch? u kidding? OH SNAP! BITCH GOT THE ROID RAGE!"
He has to concentrate to use his more powerful abilities like telekinesis, when she walked up and tore the meter straight out of his hands, he was obviously taken aback, not much chance to block a follow through from a chick who's torn multiple men in half.
I explained the detail with Hiro already, but also after watching a second time, it all happened very quickly. He shows up, yells "Sylar" and gives him barely enough time to turn around before Hiro charged him screaming with a sword. Sylar was bloodied, battered and weakened. Most of the fight was gone out of him from and he had taken a serious beating from Nikki and Peter with Nikki's abilities. It all happened at a very fast pace and Hiro's already proven that he's faster than Sylar.
Also, watch that last shot in Sylar's eyes and the sinister smirk on his face AFTER he got stabbed. I'm not entirely sure he didn't know that was going to happen and almost looking forward to it. Fatalistic types are hard to decipher, just look at Kain of the Legacy of Kain series of video games.
According to creator Tim Kring, aat least one of them will in fact be dying. I think Nathan really is dead and I have the sinking feeling that Matt will pop up briefly only to die in the hospital after some vague closure with his pregnant wife.
Nathan's role is a lot harder to explain than some of you assume. Nathan's proven he's rather intelligent. He had no way of knowing when Peter was going to fully go critical and blow, if he dumped him, there's too much of a risk of him dropping back into the city too quickly and still causing massive casualties.
I'm worried about Parkman because, regardless of his powers, he took five bullets point blank in the chest and then sat in Kirby Plaza for at least five to ten minutes bleeding. He could survive, but it's going to be very much in limbo. He's my favorite character, but the only reason I can see him surviving is because his story seems far from over.
Also, just because it's the SEASON finale, doesn't mean it all has to be final. No intelligent writer or producer kills off the majority of their cast after the first fucking chapter, and that's what this is. They've got a rough plot outline of five years, and considering the staggering popularity, it'll be around at least that long. They've killed enough big characters (Simone, Isaac, Ted, Linderman, Thompson to name a few, and at least one of the limbo deaths will allegedly result in a KIA according to Kring), if they keep going, we have to start from square one with introductions. This was all just the first of many story arcs (Season two is set to encompass at least two, 'Generations' is said to only last to about mid-season), there's too much time left to go trigger-happy on such an excellent cast.
