Other than the beginning of Lost, I don't think he's been very involved with the creative aspects of any of the show's he's produced the last few seasons.
He did write and/or direct a few Fringe
episodes, but not many. For the most part, these days his personal focus is on movies, and while he may co-develop Bad Robot's shows and often co-write or direct their pilots, he's not the main creative force behind them anymore. It's just that his production company makes them.