Season 1 . . . They originally did use the Hatian to stop Sylar. They captured him initially in Texas using the Hatian and the girl with the power of persuassion (Her power was so cool. I liked how her voice changed when she was using her power

I miss her). But remember, the power of persuassion didn't work on Sylar when she tried to have him kill himself? I think Sylar has a way of understanding people's powers and then they don't affect him anymore?
I don't think so. That would make him practically impervious. Maybe on a base level his power protects him from something like a suggestive power while his own is activating.
Season 2 . . . They didn't need the Hatian to stop Adam. Apparently all you needed to do to kill Adam was shoot his head off. That was the biggest plot hole ever when they announced that it was possible to kill a "Regenerator" by shooting them in the head. HRG was shot in the head and he was brought back by Claire's blood. But then they fixed that by saying Claire's regeneration was "better" and she is "special". But what about that huge explosion in the past where Hiro and Adam were fighting. I'm pretty sure that would have caused massive damage to his head and killed him.
Decapitation is correct. Noah was never decapitated. There is also a place in the head where their regeneration is inactive, as per Claire and Peter in the first season.
Season 3 . . . It would be too easy?
Being poisoned and put into a "coma", Arthur probably didn't have much else to think about. I doubt he'd let himself be caught by surprise again, or have some sort of countermeasure in place. Besides, the Hatian doesn't give any sort of protection for himself. Knock him out, shoot him, whatever, and he's out of the picture. And he couldn't use his power, because to protect him, other people would have to use theirs. Unless he can pick and choose, of course. We don't know a lot about the Hatian's power remember.
As for the article, the only point I agree at all with is the too many heroes part. Mainly just for Copycat girl. The others are/were necessary for each important individual's story to come together.
Time travel is a personal demon for Hiro. And it was for Isaac, although the African painter (forget his name) seems to have dealt with it in his own way. But it's a great way of exposing some plot details and foreshadowing, because the future is just that, the future. And you can't tell me you wouldn't try and figure out what to do in the present by looking at the future if you had that ability. It's something everyone could relate to, because everyone would do it.
The heroes can't use their abilities to help others, because that would set a giant flaming beacon to the Company(ies?) to come and get them. They'd have to deal with those organizations in some capacity to do something like that. But they've been a little busy saving the world and their own lives to do something to that end.
Of course the heroes are "self-involved". If I had that kind of power, I would be too. Even if they did have normal lives, it would make for terrible TV for a show called Heroes. The same person who wrote that article would be complaining about the lack of power usage and focus.
The heroes aren't supposed to work together, nor are good and evil supposed to be clearly defined. That's the entire point of this season in a way. To show that good and evil are two sides of the same coin, and it's not necessarily that these are the good guys, and these are the bad guys, because it's all perspective. And the means in which in which they accomplish their goals.
If all the heroes worked together, it'd turn into an X-Men kinda thing, which Heroes isn't meant to be.