I honestly believe that Red John is not someone that anyone will expect. I think that if you expect a character to be RJ, that character will, if anything, be working for RJ.

Also, the theory that PJ is RJ is BS. I highly doubt that the writers would actually make that happen. It is, however, a possibility that, at some point, Red John makes Jane believe that PJ is RJ.

Also, the writers definitely know who RJ is. TV Shows are not written and filmed mid-season. Things are already set and done.