I wonder if he quit b/c he wanted to take the show in a direction that the higher-ups were reluctant to go & he got frustrated.
Could be, or it could be he has the chance to create his own series/pilots and try and get them picked up. I'm sure he would rather have his own series on tv that he has full control over, rather then being a minion on another series.
I mean if he doesn't need the cash of a steady gig on Heroes, then he is better suited to be out making his own stuff and trying to get them into series. That way he will have control and even more money for being the series creator and show runner.