Finally got around to seeing it. I think it was a good finale, but not a great one. As others have noted the fight scene was a major letdown. I liked how nearly everyone got into the action in some way - all the heroes joining forces vs. Sylar - but for Peter to amass all this power and then punch Sylar a few times was pretty weak. Their fight scene in the hallway in the future was far more intense and we didn't even see it. The Sylar crawling away part, though, was nothing short of ridiculous. How in the living hell did he just crawl away and nobody either saw him crawl away or seemed to be bothered by the fact he was gone? And if he crawled away after everyone had left, why was his body just left there by the police and ambulance? This is a great show with great writing but that's incredibly lame.
As far as next season, the person who noted the Whedon-esque reference was on the mark. The man who sees Molly is likely to be the Big Bad and he may or may not be working with Sylar. I hope Peter's not dead. He has the potential to be a great character (we saw that in his future incarnation). I'm fine with Nathan biting the dust.