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.