I think there is a link between Red John and Van Pelt.

What if Van Pelt were actually the real main character of the Mentalist ? Indeed, the pilot episode deals with Van Pelt first coming to the CBI, and I'm convinced the first clues are given in this episode : she may be the key to solve the Red John mystery. Maybe the fact she is red-haired is a sign to the viewers ? Let me explain you my theory, or more precisely some interesting elements about Van Pelt I noticed.

First, she always has troubles : her strange boyfriend who is actually the killer the team was looking for, Craig O'Laughlin who is a RJ's associate, ... It looks like if she had a very bad luck. And, there is this trauma : "... you're deeply repressed and emotionally shut down... because of a trauma in your past that you've never spoken of to anyone... ever... even yourself..." that Patrick talks about in the first episode... Maybe the suicide of her sister ? A very fuzzy situation here, and we never had any answer to this question.

Moreover, she appears in almost every episode of the show and she is the one who seems the most interested in Patrick's tricks. Grace believes in High-beyond, with médiums, etc,... Van Pelt says in the dinner scene (in the pilot) that her aunt, Yolanda,  was a "real" psychic (what Janes refuses to admit). And in an episode with the leader of Visualize, she seems to appreciate the advice given by Brett Stiles.

Also, she is also specialized in data processing, and Red John proved that he was also very skilled in that domain. He intruded the CBI computers at the moment Van Pelt was on hers.

She smiles at the end of an episode when she sees PJ crying.

In the last episode of season 2, in which PJ meets RJ, RJ ends telling Patrick : "Roll Tides", which could be linked with a football, and her father, Amos Van Pelt, were trainer of football. And Craig O'Laughlin knows VP's father as he trained him at school.

To sum things up : she is red-haired, she shows up in the first episode, she has odd connections with some of the murders, she is skilful with computers, she has connections with magic and mentalism, she never talked about her trauma, her father is frequently evoked but we don't know who he is... And more !

My guess ? Red John could be Van Pelt's father or somebody in VP's family (maybe Yolanda ?). What if Van Pelt were Red John ?