After the magnificence of season one, season two was a let down. Especially that Hiro in ancient Japan story. What a snoozefest. So far this season has been better.
The time travel is getting a little out of control, I think. Hiro says he'll never go back in time again because of how he messed with the future last time, so that sets up his ridiculous plot line of the formula when in reality he could have just gone back in time two minutes and put the formula back in the safe. Meanwhile future Peter jumping all over the place screwing up stuff. It's getting a little old and is reminding me of that Simpsons episode where Homer goes back in time and steps on a bug and ruins everything.
These story lines are just getting too convoluted. They need to pick a direction and go with it. Hiro and Ando's story, Matt Parkman's story, even Mohinder and Maya, seem to take away from the central storyline, although I guess Mohinder will come back into play with his formula to give anyone powers.
I watched an alternate ending to season two on the DVDs. Originally they were going to let the virus be released and then instead of Nathan being shot, he was going to collapse from the virus. But because of the writer's strike they had to change it up. Also Maya's whole purpose was that part of her ability was to take in the virus to her body and die, thus saving the world. But since the virus never got out, now she's just hanging around. I say just kill her then.