In the season premier of the sixth season, at the end when Lisbon enters the house the door is closed in the room she finds Brett Partridge. She hears a sound and turns her back towards the door. The door is still closed. After she finds Brett Partridge and stands up, the door is open as she looks around meaning that Red John entered through that door.

This conclusively proves that Brett Partridge is not Red John.

Further, Ray Haffner is afraid of spiders and the doctor is convinced that Red John has some kind of phobia but it is not fear of heights. He is an excellent whistler. Also he is the only person who calls Lisbon by her name 'Teresa'. When PJ calls Lisbon's phone, RJ tells him that 'Teresa can't answer her phone.' He is directly connected to Visualize and is the right age to be Red John.