Ok i know your sick of reading my stuff but nobody else is posting so i figure why not.

i think i know how Dr Linus Wagner will be used in the future episode he is in.
Wagner used the services on the BA to take care of his problem. Dr Tanne his colleague, was going to put him in jail.
So Wagner called up the Ba and they took care if it for him. They used the schtick of Red John but did it sloppily.
Bret Partridge took care of the crime scene. Thats why he was so distraught when Jane figured it was not Red John who did the killings. If you remember that episode, Partridge was so excited explaining how it happened and visibly nervous when Jane tore his theory apart. Nervous is not the emotion he would portray if he was simply being proven wrong. 
The show will most likely go back into the BA and interview Wagner and i bet this is what comes out.

I have always believed that the real Red John did looked at the BA as enemies. They used his name and style for their own bidding. "Red John" is just a name created by the newspapers. The real killer has been laying low and would never risk getting caught just to taunt as jane says. (church scene seemed like rj only wanted to brag)
Thats why "red john" is dead in a way, the BA's scapegoat and entity they created is dead with Partridge and the BA  being dealt with.Yea Reede Smith lied about rjs involvement in the B.A.

side note:is it weird that one of janes clients was Amy Haffner