While I wasn't disappointed with the way the season ended, I'm like others and think that it could have been done a little better. I think Sylar is dead, or at least he died, whether or not he can come back is yet to be seen, but then does he come back with all his powers or does he need to aquire new ones? The only reason I would think he could come back is because of whomever that little girl (the "tracking system") was talking about when she said there was someone worse than the boogie man, who could see her when she looked for him, I think he might have the power to revive Sylar, or something, but I think he stole the body regardless of what becomes of it.
As for the eclipse/Galactus, my own theory is closer to Galactus, in Mohinder's little speech at the end the last thing he said was "we are not alone". This to me would suggest aliens. It's made me think that perhaps this is an all family thing. If they gave the samurai (who I agree is Hiro's father, or at the very least was being played by the same actor) powers and then he through reproduction spread the powers, it would stay close at first but eventually his descendants would mix with other cultures. Also since Hiro's father said he was the first to rise, it may be that he sought out other cultures because his offspring didn't carry his ability.
Beyond all that I was wondering what everyone thoughts are with the whole origins thing? With the voting on a new character for season 3? I'm psyched, but I'm trying not to get my hopes up, because I can also see this ruining the series all together.