It's all of them.  They are in league with each other.  One of them initiated it, perhaps Stiles or an unknown force, but each one is guilty of some of Red John's crimes.  Each of the final suspects show us different traits of Red John.  Bertram is narcissistic, Kirkland is a weirdo methodical boss man, Haffner is a charming psychopath, Reede Smith is just barely kept within his limits, Stiles has a mastermind ego, and Thomas is personable.  Each one is partially Red John, but all of them together are in league committing the murders.  It started with Haffner and Stiles at Visualize and the group expanded and began indoctrinating people.  Stiles has told us he knows more than Jane could imagine, and Bertram made an undeniable William Blake reference.  Haffner is Visualize, etc.  They work together.  It's the violent, bloody side of Visualize that has influence over the law due to roots in CBI and Homeland Security.  All of them are responsible together.  It would also explain the conversations that the suspects have together in Bertram's office several times.  

It sucks.  I really wanted it to be Manelli.