Okay, thought I'd put in one last theory before the two pivotal Red John episodes that bring his reveal and capture.
First thing's first, let's go through all seven suspects and look at why they all could and couldn't be Red John. 
Scroll to the big dashed line if you just want to read my theory about the connection between the suspects and who, in my opinion, is Red John.

Reede Smith
Why he could be Red John:
Nobody expects him.
We've seen that he can appear calm and innocent, but we know that on the inside he's a dark, twisted, angry man.
He has acrophobia, the fear of heights that Jay Roth claimed to have (6x02).

Why he couldn't be Red John:
Assuming the physical descriptions from Rosalind Harker and Sophie Miller are that of the real Red John, he's too large, too tall, and also too young.
He doesn't have the mental composure that Red John should have.
It wouldn't make sense to make such a minor character as him into the big, bad Red John that's been hyped up for six seasons.
He's acknowledged that he is a "lower level guy" which a stark narcissist like Red John would never do.

Gale Bertram
Why he could be Red John:
He holds a position of power in being the director of the CBI.
He likes William Blake. 
He has an extremely glassy, ominous look in his eyes while in the house in 6x06, and he's the only one that takes initiative in trying to calm Patrick down.

Why he couldn't be Red John:
As we see in 6x06, he still reports to somebody higher up than him about advances in the Red John case, and we know that Red John, whether or not he's the leader of Tyger Tyger, doesn't report to anybody; he's his own leader.
He has a real desire to catch Red John.
He doesn't appear to want Patrick's friendship.
He doesn't have any hair, and doesn't look like he would have had much more six years ago, when Roy was off with Rosalind Harker.

Ray Haffner
Why he could be Red John:
He fits all physical descriptions we've been given.
He has a phobia, arachnophobia.
He is an excellent whistler.
He appears to be hiding something dark (and we'll probably find out more about this, regardless of whether or not he is RJ).
If RJ was the one to kill Kira Tinsley, she made a vertical three-dot tattoo. Haffner didn't expose his whole shoulder in Jane's house during 6x06, so it's possible that he has a vertical three-dot tattoo instead of the horizontal Tyger Tyger three-dot tattoo.
His admiration for Lisbon could be the explanation as to why he didn't kill her in 6x01.

Why he couldn't be Red John:
He seemed truly offended and sad when he found out that Lisbon suspected him of being Red John.
He wants to help Patrick and the CBI team, we know this because of his dialogue with them in 6x05.
We already know that Jane is smarter than him.
The GPS bug on his phone in 6x01 is listed as being "in transit" and far away from Partridge's location at the time of Partridge's supposed death.

Sheriff Thomas McAllister
Why he could be Red John:
He already has somewhat playful chemistry with Patrick.
He likes to hunt "anything with a face".
He's been there since the beginning (first appearance in 1x02).
His job could allow him to fly under the radar and not draw a lot of suspicion.
He fits the physical description of Jay Roth, he's a good whistler, and he would have fit the description of Roy Tagliaferro about six years ago, because he did have short straight hair back then.
He has a fear of birds, which fits in with the whole pigeon theory.

Why he couldn't be Red John:
He's already sort of friends with Patrick.
He wants to help Patrick catch Red John.
He blatantly denies being Red John in 6x06, which wouldn't make sense for the real RJ to do, since RJ is an extreme narcissist.

Now we get to the more interesting suspects.

Bob Kirkland
Why he could be Red John:
He's twisted and psychopathic, and we know he has no problem with killing/torturing people.
He fits the physical descriptions of Rosalind Harker and Sophie Miller perfectly.
He likes to say his family grew up in America, which could be the carnival connection that it sounds like Red John and Patrick might have had.
Roy Tagliaferro smells of "pine, nails, and earth". Michael Kirkland owns a building that Bob uses that is in the middle of a pine forest.

Why he couldn't be Red John:
We saw him shot, seven times (or did we? I'll get to that later...).
He claims to be hunting Red John, so he wouldn't really have a reason to kill the suspects from the fake list if he was actually Red John.
Working in Homeland Security is a pretty high profile job, so it would be pretty hard for him to hide being a notorious serial killer that he claimed to be hunting.

Bret Stiles
Why he could be Red John:
He's the only person on the list, and arguably even on the show, that rivals Patrick in terms of intelligence.
He's a master manipulator of people.
There's something dark about him that no one can quite put their finger on.
He has virtually unlimited resources.
He likes Patrick.
All in all, he's a twisted, manipulative mastermind of a very ominous cult that could easily have many disciples to do his dirty work.

Why he couldn't be Red John:
He's too old and too short, if we go by Rosalind and Sophie's descriptions.
He claims to know more than Patrick or Red John could ever hope to know, thus showing that he puts himself on an even higher plane than RJ.
Assuming Red John performs most of his killings himself, Stiles' age would be detrimental to his physical ability to overtake, rape, and kill the women that RJ does.

Brett Partridge
Why he could be Red John:
He has truly been there from the beginning (1x01).
His first line is "Red John enters here".
We know that he has a twisted mind, and that he admires Red John's work.
We can infer from subtle clues in 6x01 that he has acarophobia (sounds very similar to acrophobia phonetically), the fear of biting insects.
He always suggests the opposite of what's really happened at a Red John crime scene.
He would make the most sense as the Keyser Soze kind of character that Heller said Red John is.
In 1x01, he says that he's stoked to finally see a Red John smiley in the flesh, but in 5x22, he says he's worked Red John scenes since RJ began killing. Possibly a slip-up? Also in 5x22, he states that Lorelei Martins (in reference to Red John) was an internal affair, so her death doesn't count as a true Red John killing. How did he know that Lorelei was an internal affair?
He clearly strives for the admiration/friendship of Jane.

Why he couldn't be Red John:
He is supposedly dead.
You could make the argument that the creepy forensics guy turned serial killer is too cliche.
If he doesn't put on an act to confuse Patrick, then he's a creepy, not very charming guy that wouldn't really be able to manipulate people like Lorelei.
There is a possibility that he was an RJ accomplice that was going to turn good to help Patrick.


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Now that that's all out of the way, let's get to my actual theory.

Let's operate under the assumption that the list of 7 is indeed the list that Heller said we can trust. 

We have:
Brett Partridge (age 45, short, straight hair, height 5'11")
Gale Bertram (age 51, bald, height 6'3")
Reede Smith (age 37, short, straight hair, height 6'3")
Bret Stiles (age 70, short, spiky hair, height 5'9")
Ray Haffner (age 46, short, straight hair, height 6'1")
Thomas McAllister (age 50, bald [but short, straight hair six years ago], height 6'0")
Bob Kirkland (age 44, short, straight hair, height 5'9")


Red John's first killings were at the Elliston farm in 1988, and Patrick notes that the man who saw the young RJ painting the smiley on the side of the barn would consider anyone under the age of 30 "some kid", which is how the man described the young RJ. 
Given that clue, we can eliminate Stiles, as he would have been 45 at the time.
Some might say that Reede Smith could be eliminated at this point because he would have been 12 at the time, but extremely twisted serial killers could even start killing at as young of an age as 12. 

Now we have six suspects. 

The next clue we have is Sophie Miller's description. It goes as follows:

"Preliminary diagnostic session with Jay Roth. Mr. Roth came in complaining of a recent issue with severe acrophobia. He’s middle-aged, in good health, with no stated prior history of psychiatric issues. He has no living family, but many friends on whom he relies for company and emotional support. He’s well-spoken, good posture, self-possessed. In the waiting room, he sat calmly in one place, needing no distraction.Though I note, he is an excellent whistler. His self-presentation is pleasant, but there are hints in his behavior of a damaged and narcissistic personality. He says he deals with conflict and adversity easily, though I’m not convinced he’s being truthful about this. In fact, much of what he said, though spoken convincingly, did not match what I can only call my instinctive response to his presence, though I cannot point to identifiable clinical behaviors that indicate this. I sense something deceptive and dark in his emotional makeup. However, there is every indication that his phobia issues are real whether acrophobia or some other issue remains to be seen. An interesting case. I look forward to further sessions with him.”

Now, we can immediately eliminate Reede Smith due to poor posture and self-presentation. Bertram wears a wedding ring, as well as McAllister, so we can eliminate them since Roth/Red John has no living family. Also, we've never been given an indication that Kirkland has a phobia, so it makes sense to eliminate him at this point as well.

And then there were two.

Coming back full circle to the very first season, we have Rosalind Harker's description of Roy Tagliaferro/Red John. If we can trust her description, it goes as follows:
"Just under six feet tall, with short, straight hair, not muscular but not soft, with strong hands." 
Ray Haffner is 6'1", and that is actually a very noticeable difference from just under 6 feet tall.

So who's left?

Brett Partridge.

There are some people who are saying "well, Partridge has to be dead, Patrick wouldn't just run over his death and not check the body or the crime scene, that's an insult by the writers to his intelligence!"

Wrong.

Why did we never see Partridge's body? Why didn't we see Patrick check the crime scene? What did Patrick do with the blood from Lisbon's face? Is it a coincidence that Oscar Cordero, the EMT that was first on the scene at 5570 West Huron is the same one that was first on the scene at Kira Tinsley's house? Why was Patrick so eager to contact Lisbon if all he wanted to do was make up over their argument? 


Note: before I go on, remember the fact that season 6 picks up on the same day that season 5 ends. You'll get the importance later.


Here's what I believe happened throughout these last few episodes:

The Desert Rose

Jane confronts Partridge in the desert. Flies are buzzing all around. Jane takes notice that something is bothering Partridge, but he hasn't made a solid connection yet. Partridge can tell, though, that Patrick is on to him.
Fast forward a day, the Red John suspects all have their phones bugged, and Partridge is at 5570 West Huron.
Fast forward another day, and Lisbon gets the call about persons in distress at 5570 West Huron.
Why was Partridge there for a whole day/visiting their multiple times in the span of 24 hours?
Jane is calling Lisbon as she is on her way to/searching 5570 West Huron. He calls her multiple times in quick succession. Why is he so eager?
He just made the connection to Bosco's intel on Red John from the beginning of season 2. 
Bosco's intel was that Red John has acaraphobia, the fear of biting bugs. Jane makes that connection with his confrontation with Partridge in the desert, and calls Lisbon to tell her he knows who Red John is.
When Red John answer's Lisbon's phone, Jane immediately knows what he has to do: pretend like he never made that connection, and set up a long con to draw the real Red John out of hiding.

Black-Winged Redbird

Patrick arrives at the scene where Lisbon was knocked out and painted on by RJ. He knows that most of the people there know that he cares about Lisbon, so when he goes to wash the blood off of her face instead of investigating the scene, it won't look weird to anyone. 

Jane walks into a meeting with Bertram, Smith, and McAllister. He says that Red John has killed two people in a span of days.
Hmmm....
Jane's happy memory (I forget her name)
Brett Partridge
Sophie Miller

That would be three people. Could Jane have slipped up, because he knows Partridge is Red John, so he didn't count him?

Anyways, fast forward to Patrick and Lisbon on the park bench. The mysterious woman feeding the pigeons is wearing the exact same watch that Partridge wears on the exact same wrist. Patrick notices this during his long stare towards the woman, and determines that she is a spy for RJ. He then stops Lisbon from leaving so that he can tell her about Sophie Miller's voice recorder, knowing that the spy will hear it, and report back to RJ/Partridge that Patrick is fully unaware that Partidge is alive, because he is pursuing the clue that RJ left at Sophie Miller's house.

The Red Tattoo

Fast forward to Kira Tinsley's house: Red John rushes in and cuts her up, but not to the point where she'll die before Patrick arrives. RJ intentionally bears his shoulder, showing the tattoo and knowing that it will lead Jane to pursue Bertram, McAllister, and Smith. Then Jane, the man who has been so careful and guarding of clues towards Red John, willingly and quickly spits out that Red John has a tattoo of three dots on his left shoulder to Lisbon, right in front of Oscar Cordero, RJ's EMT disciple. Jane knows that Cordero will report to RJ/Partridge that Jane is pursuing the clue of the tattoo, and thus, RJ/Partridge is fully reassured that Patrick is off his tracks.

Fire and Brimstone 
Jane continues his long con by getting all the 5 remaining suspects into a room together. He knows that this will draw the true Red John out in one way or another. Jane truly knows that Red John is Partridge after Stiles' reaction to his statement that one of the 5 in the room is Red John. We all know that Stiles is aware of who Red John is, and most of us agree that he is the father of Red John and his source of funding. 
(side note: Stiles, during his ascension ritual, draws lines of blood on one girl's eyes, and paints a u-shape of blood on the chest of the other girl. Origin of the RJ smiley?)

The Great Red Dragon
Jane reveals Red John's identity to the press as a false name, either Bertram or Smith. The police then go on a wild goose chase for whoever he names as Red John, as Jane enters the final phase of his long con, pursuing the man that he knows is really Red John, Brett Partridge. Since Partridge has already been reported as dead, then Jane knows that if he's careful, he can kill Red John and get away with it, since he's already assumed as dead.


Just my thoughts. Regardless of who Red John is, Heller has done an excellent job with the RJ saga and I'll be satisfied with the end of it, even though it sucks to see it go.

Had Walter Mashburn been on the list of seven, he would right now be everybody's top pick for red John. He is far and away the best fit, which I think in of itself is proof that Heller couldn't have a true list of suspects because it would just be far too obvious. Which is exactly why I never bought into that list.

CBI Forensic is RJ. How original.

Honestly, I don't care if the backstory is the greatest in the history. I don't care if its an intricate and a brilliantly woven story, with neatly planted clues along the way. I don't care if Red John storyline's unanswered question from every season are comprehensively answered. I don't care if Patrick Jane has played the longest, greatest trick of all time somehow.

If Brett Partridge is Red John, I will lose a freaking $1,000 bet.

It would be epic if the next two episodes played out like this.

In the press conference Jane tells the media that himself and the CBI have concluded that FBI agent Reede Smith is the Red John killer. Jane convinces everyone, including Lisbon and the real RJ, that its the truth and the media and everyone hunt down Smith, who happens to be killed before he can be taken into custody. As far as everyone is concerned Red John is Smith.

This is what will draw Red John out of hiding and into confronting Jane, he was prepared to run away and start a new life but he can't bare the thorough that someone else will get credit for his work. So he reveals himself to Jane.

Jane then kills him, but as he is dying Jane tells RJ that all the work he did will now be credited to a fat sloppy FBI agent. This is Jane victory, not only has he killed RJ but he's humiliated him as well.

Cheers