I'm okay with Sheriff McAllister being Red John. I think the writers deliberately portrayed him as a pathetic loser to avoid making him grandiose.  Can you think of anyone in the real world wanting to be just like Red John now?  Thanks!

In my mind at least one big clue was resolved.  People familar with Scottish syrnames know that "Mc" is an abbreviation of "Mac."  Perhaps in Season 1, Episode 11, the victim was trying to write He is Mac (as in MacAllister)  rather than He is Mar.

One thing that just doesn't set right with me in the reveal is the choice of weapons.  Given a choice, Red John always used a knife,  A handgun seems a little too clean and antiseptic for the final kill of his arch rival.  Then, as this is sinking in, the dark headed lady walks up and slashes at Patrick with a long bladed knife.  I think that this lady may turn into Patrick's next arch rival on the series. 

All in all, we still must remember that all of it is fiction written to entertain us and shouldn't be taken too seriously.