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.