Here's one for David Lynch fans...
Could Red John be similar to Killer BOB from Twin Peaks? Some kind of evil spirit that can manifest in different people?
It would be a big change of direction for the show, because it's always said there are no psychics, etc. But then, the show is going to have a big change of direction. (RJ case finished, Rigsby and VanPelt leaving the show, two new cast members joining, episode titles changing from red-themed to blue-themed, etc.)
More bonus out-there speculation for Lynch fans: Think about how Red John would fit in with the Red Lodge from Twin Peaks, the sinister red color of the Club Silencio in Mulholland Dr., etc.)