This isn't much of a theory just stuff I was thinking about...

Don't you find curious that Stiles was shown pouring blood over some girls and then "drawing" on their faces? That has to mean something, otherwise it would be pointless to even show it. 
I do believe that most of those who were in PJ's house are not dead. We never really see anyone die and there's much more to be explored, whether it's who placed the bomb and why Stiles (was it him that shouted?) yelled something before the blast. 

I don't know if you guys have read or at least know Agatha Christie's book "And Then There Were None". The whole plot is pretty much 10 people stranded on an island and "judged" by an unknown voice, assumed to be the house's owner. The thing is, they all die and we don't get an answer until the very end. (So sorry if I ruined the book, but it's necessary) Turns out that the killer is one of the characters that died in the middle of the plot. He carefully prepared everything to go out as he wanted, leading the police to think it was an impossible scenario. 
Partridge "dies" right at the beginning of the season, giving out an important clue. I wouldn't be impressed to see him cheat death, knowing exactly how to "act" as a corpse. We all know Red John has contacts, which would explain why his autopsy is written. The dead body we saw recently might not even be his.

I also think Red John might be an old member of Visualize, meaning that Stiles (is..) or knows exactly who it is. He claims he has more reasons than the FBI waiting for him to miss the meeting with Jane. Maybe he knew exactly what he was going into. 

After reading a ton of theories, I think my picks (for now) are McAllister and Partridge. I don't see Bertram or Reede as Red John, even though they are definitely involved with him. 

P.S: Isn't it just really messed up that Ron shows up in almost every episode in the background or saying something? He may not be in Jane's list, but you gotta admit it's weird and it can't be just because!