Well, heck, I don't know. I'm not a shrink. But, considering he was determined to release a toxic virus and kill off 99% of humanity in season 2, I think he's pretty much proven he has a few loose screws.

Masochism is bad for you in the long run.

There's the video of shooting a scene where Hiro is picking up and testing a fake sword.

There are comics?

Mr Petrelli is alive, and his ability is to suck the abilities from other people. He steals all of Peter's, while hugging him. Scared me a bit

I knew that was gonna happen and I was yellin at my TV "Don't hug that guy Peter! I don't care if he's your Dad, he's a BAD GUY!" Oddly, Peter didn't listen to me.

Tracy the 'cynical ice-machine' seems waaaay cooler than Nikki 'I've got a slutty alter-ego' I'm all for giving Ali Larter better roles. Also, I like African-Isaac

Tracy is also pretty slutty, isn't she? Or am I misremembering? I thought she hooked up with Nathan last episode. Maybe I confused that with the Nikki photo somehow.

EDIT: I probably did, wouldn't make quite so much sense with Nathan believing he saw god now.

And no, Tracy is super slutty. She had sex with that other politician dude, was it the governor? For perks, I think. And I dunno, I can't remember if her and Nathan did it or not, but I'm glad she has the sluttiness ingrained into her default personality. Having it right there keeps us from requiring like half an episode's set up time just so Tracy can get her jig on.

1. Too bad Adam Monroe crumbled to dust, he's not a bad character. Then again, anybody can come back in this show anytime, from a different timeline.
2. Hiro and Ando are still dumb goofs. The success with the fake sword trick was just a fluke.
3. Peter can be so dumb. He's the main protagonist and he's kinda cool character, but damn, he's naive.
4. The whole soap opera thing in Claire's family sucks.
5. All Nikki and not-really-Nikki characters suck. And there's still one clone left, potentially.

6. Why did Adam disintegrate but Peter didn't? I hope there's some explanation for this.

Because Adam had been immortal for hundreds of years and his superpower was the only thing keeping him alive. So when the regeneration was stopped, he died. Doesn't necessarily make sense but it's been run that way in comics and so on several times.

Also, I have this suspicion that Nathan is going to turn out to have some kind of "meta" power later seeing as both his brothers and his dad did. And the flight one was chemically induced.

Maybe he will, Peter didn't show any kind of power until now. But Peter didn't get a formula shot, which means they must have known he's got it. That would mean Nathan's potential power isn't easily accessible like Peter's and Mr Petrelli's, maybe somewhat similar to Sylar's.

Well, this is part of the show I'm not sure about. How did they tell who did or didn't have powers? They hadn't come close to mapping the human genome when they were born, much less the mutant genome. And how come they gave Sylar away in the first place? A lot of these things seem like actor-budget-related retcons, like they were going to do a bunch of such plots with new characters but since the original team was so popular, tried to work it all in there instead.

It would be easy to determine Peter's power when he was a little baby considering there were probably many people with powers around. He'd just pick some and do something visual.
About Sylar, no idea.
Even if they are having trouble with plotholes or coming up with explanations, they still need to make it all make sense in the end.