I have two possibilities;
First is Jane, there are many hints in the show that make it seem as though he has a split personality or has had a psychological break. They are too many to recount and often subtle.
But my new pet theory is Abbot. He has been manipulating Jane since he was introduced and kind of orchestrated Jane and Lisbon getting together at the end of this season. If I am right the next season will feature Jane and Lisbon getting closer and then she will be murdered by the reemerged Red John.
Abbot (Red John) wants Jane and Lisbon close so that he can inflict pain onto Jane. In the past Jane may have wronged Abbot unknowingly, or represents the archetype of someone who wronged him. Abbot will eventually reveal himself to Jane, because he wants to rub his nose in it - "I did this to you, because you wronged me. I beat you!"
Like I said these are both just pet theories and I cannot wait to see what they have in store for us. Just found this site, and I am going to read all the theoeries you fine people have.
