Everything points that Red John is Bret Stiles. He is powerful, well-connected (he manages to free Lorelei form a federal prison), we know that he possibly killed someone for his cult. Knowing the location of Kristina Frye is another reason, because he wants Jane to suffer and Red John "killed" Kristina Frye (not physically but he destroyed everything she meant).
Like Lorelei said, Red John and Patrick Jane are very alike, but no friends. Bret Stiles manipulate the persons from his cult and even Van Pelt. If RJ is Bret Stiles the way he gets to Lorelei (kills her sister to make her vulnerable and manipulate her) is similar to how he gets to Van Pelt (sacrifice O'Laughlin to make Van Pelt vulnerable)
Everyhting points to Bret Stiles, BUT something isn`t right. Why would Bret Stiles come to the farm from "Red Barn" and the others would called him "kid". The age isn't right: in 1988 Red John would be somewhere between 15-30 years old, that means that now, RJ is between 40-55 years old, but Bret Stiles looks older than 55 years old. And also Rosalind seems a very young woman and she would have said something if Roy was a lot older than her.
And another reason: why would the people from Red Barn called Bret Stiles "some kid". From how we know, Bret Stiles was always the leadear of Visualize (because he allegedly killed his superior). Even if he wasn't the leader he was a very important person in Visualize and he wouldn't pass from the farm known as a "kid". And also, the priest who told Jane that some kid painted the smile, surely knows that Bret Stiles is the leader of Visualize and he would have reacted differently.
That's what I think. Although there are very powerful reasons for us to think that RJ is Bret Stiles, the "Red Barn" episode makes this theory implausible. Such a complex script couldn't be so contradictive.
Sorry for my mistakes :)
