Here's why I don't think it would be PJ.

Think about the ramifications of Red John turning out to be Patrick. It would be a defense attorney's dream. Every single case that PJ helped clear over the course of the show would immediately up for review and retrial. Almost every defendant and their attorney would be able to claim that they were framed by PJ/RJ.

Don't forget shadow of doubt here. my defendant was framed by the notorious serial killer Red John, who happened be a consultant for the CBI and worked directly on his case. would any jury need more than that to acquit.

What about evidence, every piece of information or evidence that PJ helped them obtain in the course of an investigation is now suspect and most likely wouldn't be allowed in a new trial.

PJ turning out to be RJ would kind of be a betrayal of the whole series. This all works equally well for the lisbon theories.

Lets not forget the careers of every member of that team would be effectively over. Can you imagine the final scene of the series with the head of the CBI congratulating Lisbon and her team on capturing Red John and in the next breath placing them all on suspension pending an internal investigation.

Red John is known to have accomplices. If PJ turns out to be RJ would anyone believe that the members of Lisbons team were not accomplices. even if they were cleared that specter would follow them for the rest of their careers.

PJ as RJ would be the worst ending to the show.