I'm guessing Heroes suffered from having a pre-planned plot worked out in advance that ended with season 1... that made a great arc. It wasn't suited for a follow-up and they've done an even worse job than necessary. I suppose if they'd thought of it as a sequel and written a second self-contained arc it could have turned out a lot better. Okay, that doesn't really explain what happened though. I guess what looked like good taste/judgment/writing in season 1 was actually luck, sort of like with SGA or something.