Heller anticipated that viewers would eliminate suspects one by one as they are being featured in each shows. So he plays a game and features McAllister early and uses a dramatic moment where the sheriff rescues PJ from a tall height. Viewers conclude he cannot be the suspect because RJ is afraid of heights and because he rescues PJ.

However,.....

Heller has assured us that it is one of the 7 (well, now 5)

RJ could easily have PJ dead but keeps him alive. So too does McAllister with his rescue
RJ would not show the outward antagonism towards PJ that Stiles, Haffner, Smith and Bertram. The only suspect that seems to be friendly with Janes is McAllister
A hillbilly Sheriff seems so distant to a sophisticate like RJ but that's what makes it interesting
We have been 'conditioned' to hate the Visualize cult so anyone associated with it is unlikely to be the 'real' RJ
Stiles is missing so he is too obviously being dangled as a 'likely' subject
Bertram is too uninteresting a choice since he would the be tangled up in the banal 'conspiracy at the CBI top' and this might disappoint viewers. Bertram, Haffner can then be crossed off

Partridge is dead get over it people..bruno heller isn't stupid why would he have a character fake his own death? partridge was a red herring just like kirkland was. now lets look at the list in order minus partridge & kirkland (pay close attention)

Bret Stiles first appearance season 2
Gale Bertram first appearance season 3
Ray Haffner first appearance season 4
Reede Smith first appearance season 5
Thomas McAllister first appearance Season 1 
The list is in order until you get until mcallister. he's the only one out of all the suspects to not appear at all in a rj episode minus season 6 ' he's never even mentioned red john that's because he is him..if red john is actually on the list then He Is Mar (M)c(A)lliste(R)
#ThinkAboutIt 

comment if you want my thoughts on the tyger tyger conspiracy

Don't know how I'm going to make it through this week after watching the Fire and Brimstone promo, it looks so good!! My bet is either McAllister or Bertram despite their baldness, with Ray being the dark horse. The chemistry between the Sheriff and Jane was excellent when he saved his life, so I think he'd be a satisfying reveal. Also the thing that really struck me was his pointy, heeled shoes. It isn't categorical evidence, but I think they are the closest match to the pair Red John wore, way back in the season 2 finale. He's an excellent whistler, possible fear of birds which everyone keeps mentioning, middle aged (in fact Bruno has made the character younger than the actor, so he fits closer to the RJ profile) very light footed with quality hunting and shooting skills, and most importantly the actor Xander Berkeley is very talented and is apparently experienced at playing villains. Lastly, if you watch the promo again, McAllister is the only one sitting with his legs crossed similar to the way Jane does. Not sure if that means anything but...

Besides the major clue of the tattoo presented in this episode, another subtle clue was shown. Why would Red John need to bug the CBI if he could easily assess the HQ himself. This means that RJ does not have easy access to the CBI. This leaves two viable suspects McAllister and Stiles. McAllister is RJ

S2 His red right hand start at 1:11 http://www.youtube.com/watch?v=1otRlA3PedI pay attention to the walk

S6 Black winged red bird start at 3:34 http://www.youtube.com/watch?v=772FU_fAjj4 pay attention to the walk

Also the uniforms are very similar. 

Also he has a possible phobia, very stealthy, self possessed and pretty intelligent, he does meet Rosalind's physical description, his character is meant to be 45 years old so that could put him in the age range for the 1988 barn murders, RJ smells of pine according to Rosalind and McAllister is the Sheriff of Napa county a very rural area, there's the unexplained police car at the end of the S4 finale could be his, plus it would not seem out the norm for McAllister to be walking along those corridors where Rebecca gets killed, it would take a hefty explanation for some of the other suspects (especially stiles) in how they managed to get into the cbi in a police uniform without being recognised/stopped etc.
 
There's probably more that I haven't listed and some of the clues i have given may prove meaningless, but as small/simple as it may be, it's that walk.If it is McAllister, this isn't a clue for the show's characters, it's a clue given to us the audience.

I just think more of our RJ questions are answered and more are easily explained if McAllister is RJ.

Not to be mean, but some people here either need to get a job or a girlfriend? Way to much time on your hands.

Here is my Simple Theory..

In fact i'm not sure 100% of who is Red John , BUT...
In S06E03, at 03:35 Sheriff Thomas Mccalister came , and began to solve a case with jane ; The weird thing that they are alike , they solve the case by observing and getting conclusions faster. He is clever..
I think it's a link between RJ's phobia and Pidgeons.

  Pigeons appear 3 times: 

in the s06e01 (when Lisbon enter to the house , when Partridge was killed)
and
in the s06e02 ( when Jane and Lisbon stayed in the bench, and a woman next to them give some eat to pigeons)
and
 in the s06e03 ( Mccalister, when scared about Pigeon touches him , said, i hate Pigeons )

Plus Bruno Heller told us a big clue is in the first episode : It could be Pigeons.Sheriff Mccalister is a clever man , fits all the descriptions given and hates Pigeons.