Ah well, at least Heroes made it farther than The 4400, eh?
First, a caveat: I have not, as of yet, watched Heroes this season. Not that it really has any bearing on the post I'm about to make, but I thought I'd throw it in, for the sake of full acknowledgment.
I think that there's an interesting parallel to be made between Heroes and The 4400. Both of their first full seasons were pretty good. I say "full seasons" because the actual first season of 4400 was the mini-series. However, after that, they both started to go significantly downhill. I think the reason for this is that both shows tried to do the same thing: keeping the formula the same without significantly altering the plot. Sure, there were episodes here and there that moved forward (more so in The 4400, IMO) but overall neither seemed to have a focus towards its endpoint. All they could manage were more ways to increase the number of powers.
There's a story I recall the writers making about The 4400, regarding the miniseries. The twist at the end of the first season wasn't originally going to be shown, but held back as the "series secret," so to speak. When they didn't think they'd get a second season, someone decided that the twist should be included. It turned into a great ending for the miniseries. Writers, and specifically IMO the writers of Heroes and The 4400, were too scared of revealing secrets, especially those that would move the plot significantly. I think this is born out of a justifiable fear that if you change things too much, you'll lose viewers and be out of a job.
Anyway, I think it's an apt comparison between the two shows.