I think a lot of people misunderstand the story. Why a lot of you thinking that Jane and Red John knows eachother from a long time, e.g. when they were kids? I think RJ started to kill not because of Jane, but Jane wanted to stop him/her and hurt the ego of RJ.
My theory is that something misterious happened in the house of Jane. Maybe somebody shoot the sheriff, e.g. Haffner or Stiles. Or Jane released them, and only focused on the 3 with tattoo's. Or faked this all, it was only for Red John, and he didn't want to hurt either of them, even if they are mad. I think that something is like that.
But my main suspect is Grace Van Pelt or Rigsby. A read that at least two people will prove to be smarter than we think. I think one of them will be Rigsby. I read a lot of theories, so my thoughts are in a whirl.
Let's see what happens!