I have been watching since day 1 (and have owned and watched all seasons multiple times). I've followed this site for a while all while watching the show, and it's been fun reading everyone's theories! Most people (ahem, most) have good food for thought even if I disagree.
I have thought that Red John is Brett Partridge for a long time. I initially thought it was Brett simply because he has been there for every Red John impostor scenario. He pushes and pushes that the murder "is obviously Red John" when it is clear its an impostor - See S1.E1 (Pilot), S2.E23 (Red Sky In the Morning).
Red John is experienced, yes, no arguing that. There was a while where I thought Brett Partridge might be too young. But judging by the little snippets of video we get from S2.E8 (His Red Right Hand) when we flash back to him with Carter and Janet Peak, as well as Rosalind Harker's description from S1.E23 (just under six feet tall, with short, straight hair, not muscular but not soft, with strong hands), as well as his size from S2.E23 (Red Sky In the Morning) from when we see him with Jane, we know that he's a thin guy, not tall or large.
The episode where I believe to be the most evidence is actually this past season, S5.E13 (Red Barn).
I believe Brett Partridge is Bret Stiles' son. And I believe that he is a Visualize member gone rogue, during his stint at the farm that is reflected on in this episode. I believe this is why Bret Stiles claims to know more than Jane or Red John will ever know (S3.E3 - The Blood on His Hands) and he knows somewhat, what Red John's moves are and will be, but not enough to catch Red John, and since he is his son, another reason why he may not want to give him up. I also find it interesting that although their names are spelt different, they have the same name.
I think this also makes sense with the infamous "He is Mar" which I believe to be "He is Many". Signifying a group and not just one. Though RJ himself is one (and how incredibly lame it would be if it were more than one) I think that this for me was my first clue after looking back that Visualize plays a role in this somehow, with a member gone rogue.
For anyone arguing that Brett Partridge isn't 'important' enough in the CBI - If you watch S2.E8 - His Red Right Hand - at the end of the episode, we see someone walk down the corridor whom Rebecca smiles at as if he is Red John. If this was someone more important, he wouldn't be wearing a policeman's uniform, and people would have recognized him leaving after he poisoned her. He had to be just unrecognizable enough to do that without being questioned by anyone in the building in any way, but recognizable enough to get CBI access. I also think that Red John is the kind of character who likes to hide among the "average" and not stand out as an important person in the CBI, sort of hiding in the shadows I suppose.
A few small notes:
-I think that Van Pelt has been hypnotized in some way. She is left alone with Bret Stiles during his small stint in holdings S4.E16 (His Thoughts were Red Thoughts) and after this she has somewhat of a rosy view on Visualize. In S5.E13 (Red Barn) she's speaking to the pastor about the cult, and says something odd about Visualize (off the top of my head, something like "What's wrong with wanting to be the best version of yourself you can be ::smile::") and the pastor gives her a funny look, almost like she is a part of Visualize or something. I don't think she is a RJ accomplice, but I think that this will play into the story somehow.
-I believe that even thought we left things at the end of S5 that Jane is "behind" Red John, I believe that this is a trick. I believe Jane is actually not behind him, and he is in front of him and it will be revealed at some point :) Just a hunch, since Jane always makes everyone think he is behind the game when really he's right in front of it.
