It seems obvious that it is McAllister, because the show has changed the title theme of Red to other colors - after Mcallister was killed by Jane.  The show's first episode contained a Red John tie-in.  Dr. Linus Wagner pretended Red John killed his partner & a woman.  The second episode revealed Mcallister - who was a sheriff that uncomfortable about Patrick Jane.  In the first episode, Wagner pretends to not know who Red John is.  In the second episode, McAllister pretends to not know who Jane is.  The theme is guilty minds can't keep a secret forever, there are tells that are visible to observers like Jane.