I read the comics -- I hope they didn't just kill off Hana Gitelmann, but I don't see any way she could have survived that. So lame -- they killed a character who got television screentime in the comics. :/ Perhaps she'll live on as the ghost in the machine ...
A lot of fans are complaining about the finale, but I think it's unwarranted. The finale could have been better, that's for sure, but I don't think it was bad at all. It's just that we've seen such great episodes in the past like 5YG and Company Man, we expect the quality to be outstanding more often.
The ending was very similar to Back to the Future Part 2, IMO. It's anti-climactic, appears to serve as a conduit into the next chapter, and the time traveling characters, by accident, end up in a distant past of their personal preference (Doc Brown expressed nostalgia for the wild west, Hiro Nakamura seemed very interested in the years when Samurai were rampant and going strong).
I think Sylar's TK push against Hiro supercharged his ability to bend time and space, which is why he jumped 335 years into the past, across the globe. I also think that in order for Hiro to jump back to the future, Hiro will need to make a similar event where a special from 1671 can "charge" Hiro so he can jump back to 2006 (or is it 2007?).
Nathan dying is a little sad, but if the circumstances of the finale event are ever publicized in the Heroes world, it'll be positive for the specials, since a newly elected congressman sacrifices his life to save New York City.
Sylar -- I don't think he crawled into the sewer. I think he was pulled in, by the bigger threat that Molly was talking about. I believe this bigger threat will revive Sylar, and the two will have this master/henchman relationship similar to Palpatine/Vader and Unicron/Galvatron (Transformers the Movie 1986). We will possibly see something mid/late season 2 where the Heroes have to join forces with Sylar to take down the greater threat, but it will be a very temporary alliance with a lot of tension.
When I saw the sewer scene, that Vanilla Ice Ninja Turtle song quickly came to mind.
Hiro -- When someone asks Molly Walker the whereabouts of Hiro Nakamura, I want her to walk to a nearby bookcase, pick up a coffee table sized Japanese history book, and put a pushpin in Kyoto, on a historic map that says "Japan, Tokugawa shogunate, 17th century" or something like that, then cue Hiro's first new scene of season 2.