A lot of structure of the story line makes Jane look suspicious towards being Red John. If the theory he used to catch the San Joaquin serial killer in Season 4 is applied to Red John, Jane fits in perfectly. He is self- obsessed and likes to make Red John look smart in the eyes of the public. His participation to help the police could have two reasons- to keep the legend of Red John alive. Second, because he is guilty of killing his wife and daughter, something he had to do when Patrick Jane was becoming more believable to people than red john.
He makes the blogger of the serial killer to put down Red John on a TV interview just so that Red John can come out and kill him? Why would he want to give away his one advantage where everyone believes he has killed Red John to punish the blogger (the killer). Because he does not want any other serial killer to look as smart as Red John.
Also, when Red John killed Partrick's wife and daughter, he left behind a note, this time there was no note to a man demeaning red John. Later in the season Jane loses his memory for one episode where he is shown as a womaniser and a con artist with no conscience. He says he wears the wedding ring to get sympathy from the women he cons. He also jokes with Cho about his family, which makes the entire story of him even having a family suspicious. What if he never had one, and it was all just a legend he created.
Finally, all the money that he made of coning people must be used to keep his own agents who would be carrying on their roles apart from his hypnosis technique. Hence a lot agents would further have people working for them, eg- O'Laughline or Loreli. Which is why they don't recognise Jane.
