Originally I supported Ray Haffner as Red John, then you all had me convinced that partridge was going to come back to life.  When I saw the leak I too couldnt believe it was McAllister.  He is barely in the show.  Watch the main episode that he was in again and it will make more sense I promise you, season 1 episode 2.  See hownhe watches PJ so closely, see how he changes when nobody is watching, see how the cops respond to his aid, see  how he tries to kill van pelt.  Its him alright.  He lays low after that, this also shows why he takes an interest in pj after the start of episode 2. He acts through his network after that, but notice that his close friend dubar was also a sheriff.

watch older episodes again knowing who red john was and it begins to make more sense. Just think of the clues in a practical sense rather than a hunt for bigfoot or aliens where we are drawing crazy conclusions all over the place.