Well, time for me to add in my two cents.
It was a very good ending, although we didn't quite get the answers we were promised.
In a way, I guess we were told that Charles had a power, obviously a bit like Sanjay's from earlier, sort of a dream guardian. Which is why he spoke to Peter when he was knocked out/passed out, etc...
And it is safe to assume that Mama Petrelli has a power, after all Charles and Linderman did, so she must to if she was working with them.
The only one I'm still confused about, in terms of parents, is Kaito Nakamura. Something makes me think, that he wasn't working with the company anymore. Considering Linderman seemed to be in control, and wanted New York to explode, whereas Kaito wanted Hiro to stop the bomb.
Not to mention both of them used the phrase, "We used to work with others, until some of them lost their way."
So the two camps could very well be like this:
Pro-Bomb: Linderman, Mama Petrelli
Anti-Bomb: Kaito Nakamura, Charles Deveaux
Does that mean that the "older generation" of Heroes split recently, in terms of wanting to see the bomb happen and those who didn't think it was necessary?
It also explains why Linderman, who worked with Mama Petrelli and Charles, would refuse to heal his dying friend.
But yes, hopefully those questions are answered.
Call me crazy, but I think I'm going to throw my hat into the rumour mill that Kaito Nakamura is actually Takezo Kensei...We'll see when the Blue Armoured Feudal Japan Warrior removes his mask...But until then, that's my belief.
In terms of the questions I've seen here, allow me to try and answer them.
Question: Why didn't Peter fly himself?
Answer: Peter was losing control of his abilities, hence why he exploded. As such, he couldn't access any other powers, such as flight. Also, in his current state, getting shot would likely have killed him as he wouldn't be able to control whether or not he could regenerate.
Question: Why didn't Micah yell during the fight between Niki/Jessica and Candice?
Answer: Candice is an illusionist, she alters the reality around her. For all we know. Micah was screaming his head off during the entire battle but Candice has the ability to block out sounds and sights that she doesn't want her targets to see and hear.
Question: Is Sylar dead?
Answer: No. The blood trails goes to the sewer, so Sylar was dragged down there or crawled there himself. Chances are, he did it while everyone was looking up into the sky. However, there is a smaller chance that Molly's greater villain (The one who can see her) helped Sylar escape for whatever reason. The most popular theories are it's Claude or possibly Mama Petrelli who helped.
Question: Are Nathan and Peter dead?
Answer: More than likely. Depending on how high Nathan took Peter, they could both be killed. Also, if Peter did lose complete control of his abilities, he might not be able to regenerate after he goes boom. As for Nathan, there's a small chance he might simply have flown Peter up high enough, let go, and flew away as fast as he could. We'll have to wait and see.
Question: What will happen to Molly?
Answer: Chances are, Mohinder will look after her. I know people are saying Niki and D.L. will take her, but given her condition and Mohinder's protective stance of her, it will be more likely to see Mohinder "adopt" her. A less than likely one would be Parkman recovering from his wounds, and adopting her in addition to his own unborn child.
All in all, it was a good finale. Although, I wish more questions had been answered.