Let's face it, the show peaked with the flash forward episode. That was the episode where all the character arcs really converged and the various storylines paid off. Perhaps they should have just stopped there. Since then they've wasted time and wasted their best characters, either leeching the show of drama, undermining the show's premise, or setting things up for season 2.
The worst part of the entire finale was the big showdown in Kirby Plaza. In a word, it was just awful: Sylar can stop bullets but he can't stop a sword. Peter can instantly borrow Niki/Jessica's super strength but he can't re-borrow Nathan's ability to fly. Sylar can control the nuclear ability but Peter can't. We saved the cheerleader so she can blubber and not shoot a gun. The whole world converges on Kirby Plaza but noone notices Sylar crawling into the suddenly convenient manhole. And poor Nathan. He desperately needed a character moment where he could sacrifice himself for the greater good, but the circumstances didn't warrant his sacrifice.
Overall, Heroes is a good show and with the upcoming Heroes origins show they'll have a fantastic opportunity to expand the Heroes universe. But I think at this point they have sacrificed the drama for comic book longevity. Moving forward nothing is going to have the impact of discovery that we saw in season 1. The twists and turns of HRG and Claire's family drama. The slow emergence of Sylar as a super-villain. The quixotic wanderings of Hiro and Ando.
Hiro is now in 17th century Japan which is both an "oh cool!" and an "oh, please". It's like the last five minutes of Evil Dead 2. It's just a goof. Completely meaningless. It has nothing to do with the premise of the show. Nothing to do with ordinary people living through the anxieties of extraordinary times. That was the post 9/11 mood that the show tapped into. The comic book stuff was just a way into the deeper story. Now it's an end in itself. Season 2 promises that Heroes will be just another blockbuster entertainment like Spider-man, Pirates of the Caribbean, and Shrek. Big, loud, fun-like without actually being fun. Ultimately hollow.
If they'd really wanted to blow us away here's how I would have ended it: Realizing that Peter is about to explode, Hiro embraces him and they teleport away from New York. Now they are both in feudal Japan and Peter's going to explode. How can he save the past and learn to control his powers before it's too late. Save the Samurai, save the world!