I think it is Ray Haffner.  Here are my reasons why:
First, he is a good whistler and so is Red John.
Second, he is a member of Visualize and Red John is a member of Visualize.
Third, Ray Haffner has feelings for Lisbon and Red John may have feelings for Lisbon too.  Otherwise, Red John would have killed her.
Fourth, remember Lisbon's dream in season 6 episode 2?  Well, he was in it.  In fact, he was the last person in it.  He did hit Teresa Lisbon in the dream.
Fifth, Red John is middle aged and so is Ray Haffner.
Sixth, Red John is not strong but not weak either.  Ray Haffner was lifting medium sized weights in the second episode of the sixth season.  Therefore, he is about average strength.
Seventh and final reason, he did shake hands with Jane and so did Red John probably.
Now, let me give reasons to eliminate the other suspects:
First, Reede Smith is a little too fat and too strong.  Red John is not fat nor strong.  However, Reede Smith could be an accomplice though.  
Second, Bret Stiles is too old for Red John but he could be the father of Red John.
Third, Gale Bertram is bald.  Red John is not bald.  However, he could be an accomplice though.
Fourth, Sheriff McAllister is a little too old for Red John.
Fifth, Brett Partridge is probably dead.  In fact, the actor who plays Brett Partridge says that his character is dead.  However, he does have the voice, creepiness and the intelligence of Red John.  He also has the height description of Red John and is middle age like Red John.  He also did say "Tiger, Tiger" to Lisbon and Red John has said "Tiger Tiger" to Patrick Jane.  If Brett Partridge managed to fake his death, I might change my guess back to Brett Partridge.  But I doubt it.
Sixth and final reason, Bob Kirkland talked to one of Red John's accomplices.  The accomplice does not recognize Kirkland.  Furthermore, he did not leave a smiley face after killing the accomplice.

The only top two suspects on my list are Ray Haffner and Brett Partridge.  The other suspects I could eliminate.  I am leaning towards Haffner now but I am not ready to eliminate Partridge yet.

So that is my theory.  Please rate this theory.  I would appreciate it.

The things we know (or think we know) about Red John really don't help us figure out who he is!  Sure, we have lots of details, but they just lead to grand theories of speculation.  No wonder RJ hasn't been identified by law enforcement, let alone caught.  Bruno Heller has given us reasons to suspect all 7 final suspects (and even reasons to suspect people who aren't on the list).  I think Patrick knows 100x more about RJ than the most die hard Mentalist fans.  If the Mentalist were a book, I'm sure we would get insights into his thinking that are hard to convey on tv.

Last point, do we know for sure it was RJ in the season 2 finale?  It could have been one of his followers.  Just like the season 3 finale, you think timothy carter is RJ, but he can't prove he is RJ!  I'm sure RJ has bragged about his murders and he told Timothy Carter how to make PJ think he really was RJ.  So i guess it leads me to this question: When Red John is revealed, how do we KNOW it is him?  Cuz i'm assuming they can't just go but what he says, dna, descriptions from others, etc.  However, I trust that PJ will figure out a way to prove he is RJ, so he doesn't get tricked again.

I think that Brett Partidge was the Red John killer (the individual who actually did the killing) and was either the son of or connected with Bret Stiles since a very young age (as he was the individual on the Visual farm we learned about last season). Now, Stiles would want to protect his son/apprentice (whatever he is) so he used his influence with the church and his money to buy off FBI agents, recruit church members, and put people in positions of power to help protect Partridge (Red John's disciples). These people include the likes of Gale Bertram, McAllister, and the other suspects. However, despite their promises to Stiles to protect Red John (Stiles may have helped them get there positions in law enforcement, etc.), as Jane narrows down the list to 7 suspects they realize that their plan has become too risky and they may all be implicated. As a result, they decide to kill off Partridge and the people who have information that could incriminate their entire group. So, they lured Partridge to the house with a promise he could kill Lisbon and, instead, killed him. Then they had one of them call Jane (using the voice changer Partridge used for his Red John voice) and say the line "Lisbon can't come to the phone right now" (thinking that they've covered up all the evidence and are sending Jane on a wild goose chase for a serial killer who is already dead). This would explain why "Red John" didn't kill Lisbon, because it was Bertram and Haffner and the others...all people who like and respect her.

Of course this is all speculation...but it does explain the "He is mar" clue as "He is many". It could also explain the conversation we just saw in S6E2 where McAllister and Agent Reede are talking to Bertram and ask him "how much Jane knows"...hinting to the fact that they're all involved somehow. Bruno Heller has also said that following the conclusion of the Red John storyline, the show will have another direction to go in (and the conflict with Stiles and Visualize could be that direction, as Jane didn't get his chance to exact revenge on Partridge/RJ so he will want to exact revenge on those who enabled him).