I think the problem with season 2 was that they really hadn't decided how they wanted to continue. When they were first talking about the second season, the idea was to have a completely new cast of heroes, with maybe a few returning from season 1 in order to bridge the show. That way, they could have the same "discovering powers" stuff that worked for season 1.
The problem was that they also realized that they couldn't get away with dropping popular characters like Sylar, Hiro, and Peter. So they got stuck in some failed attempt to have their cake and eat it, too.
Hopefully they have a better idea going into next season of what they really want to do on a year-to-year basis.