It would be a great twist if Bret Stiles, Thomas McAllister and Krystina Frye were all involved in the Red John case. Bret Stiles would be the great leader behind all cases. Their beliefs justify what Red John said at the end of the fourth season, he would not be sentenced for his crimes. Due to the psychic powers of Krystina, there would be an explanation of how Red John knew the names in the Patrick Jane's list. Finally, Thomas McAllister would be Red John, the person who execute the plans. There is some evidence in the series that Bret Stiles would be involved, for example, it was him who gave the whereabouts of Krystina in third season. Moreover, Red John didn't kill Krystina. Of course these are just some thoughts and the series certainly would not take that route.