Red John as being the alter ego of our dear old Patrick seems to be the most plausable solution now. It's been the same game of chess between the "gold" and "black" part of the tiger in its "fearful symetry," at least if we believe in Kimbals interpretation of Blake's poem.

This is the most plausable solution for many reasons and we can name a few:

1. Red John is simply to perfect and infallible and knows even Jane even better than he knows himself. Jane feels thus dark presence and fears it.

2. We don't know much about Jane's previous life but its still enough to determin that he had an unhappy and disturbed life even before the demise if his family. IRS playsable to assume that Red John creates his cult demanding a sacrifice of loved ones as a means of emerging ones "true identity" - thus he also has a leverage over new disciples.

3. Furthermore, no one in the series has such power of manipulation and influence on people - especialy hypnosis. Dark twin is the only probable explanation for creating such elaborate network of manipulation and blackmail (with likely victims being powerhungry individuals as Berthram and Styles, or pure psychos as La Roache or Kirkland).

4. Besides PJ is the "unlikeliest suspect" especially as our attention is being diverted (in accordance with tradition of both magical tricks and crime dramas) to no less than 7 other suspects, who however are likely willing or unwilling accomplices.

There are numerous other references to this possibility like Styles "knowing much about Red John" (who was associated with the cult and might even "help" his rise to power by murdering the opposition). Besides, close circle of Red John followers is bound to know about the "Jane" persona and is probably dedicatet to protecting their master from himself even up to a point of willing sacrifice in order to preserve him. As for the handshaking part its either an elaborate decepcion or a symbolic act of acceptance of the "tiger duality" after the murder of his own family and full separation of his true identity.

Finally even if all this is revealed by the half of S06 its not necessary the end because Jane/John might continue to solve cases from an insane asylum thus taking the role similar to Hanuval Lector.