Do we know if Red John was only a member of Visualize when he was young in the 80s or if he was in the cult even as a 'grown up'? 
I don't know why but I always thought Red John had some kind of respect for Bret Stiles especially if he was still in Visualize and that he would never kill his 'guru'. But McAllister didn't even care about killing him for a second. Maybe I'm too sentimental because in my mind even if RJ is a psycho, he wouldn't kill the person who helped him so much in the past that easily.:D 

So either: Red John is not McAllister and/or Bret Stiles is alive, or: he was McAllister, Bret Stiles is dead and this is just one of the million things that we didn't get an explanation for..I hope it's the first option. I want Bret Stiles to be alive so much!:)

1. Sheriff was no the Red John.
2. The important part happens during the two years ( missing since the sheriff's death)
3. Jane kills the sheriff and allows the others to believe it's over, so he can go after the real Red John. It takes some time to track him , infliltrate his surroundings, and perform his biggest act yet - taking everything he has. His memories, his personality , and his powers - leaving him a mental wreck - the guy who you've seen sitting at the bar on the beach - Roger. Even if he didn't look exactly like Stiles, that's what happens if you take someone's persona and the spark in the eyes away - the most grandious performance of Jane's life. Patrick Jane is a Monster.

There's no way Stiles and Haffner just die off screen and are never mentioned agian.  They have to show what happened at Jane's house when the camera cuts away before the explosion    that's where the Jane/Mentalist twist is             McAllister is not Red John just another Timothy Carter  and Timothy Carter was a more convincing Red John than McAllister   there has to be more proof than a one time character just showing up and saying they are RJ     this New Beginning is just a huge misdirection     what's the logic?  it's not like RJ dominated the show  one or two RJ episodes and the finale       how is the RJ story ruining the show       without the RJ storyline The Mentalist is just another murder procedural          jane's life after RJ's death is a DVD bonus featurette or a bunch of mini webisodes    not the last season and a half (if there is a season 7)    untill the end of the season I still believe Red John is still alive     the list and the explosion is just RJ playing with Jane         why let him live after the explosion if you are just gonna kill him the next day   RJ is just toying with Jane        

I think Heller has something awesome planned for the last third of the season.  I think something more happened in Jane's house when the camera cut away.  The fact that they don't show what happened is a huge clue that we haven't seen the whole story yet. There is some kind of Mentalist twist yet to be played.  because nothing since the explosion has made sense or even felt like The Mentalist                   the only one in the show that has even come close to Red John is Patrick Jane       Patrick Jane has been there since the first episode(Jane going to sleep under the RJ smiley face)          Jane has had a fucked up childhood(we haven't even seen all the trauma)            Jane has had a mental breakdown(multiple personality??)                  Jane has a sleeping disorder          RJ is supposed to be Jane's equal but evil   Jane is playing a game with himself         He's already killed two "Red Johns"     not only has he killed two men in cold blood he has gotten away with it        Jane killed his family and to deal with it he has created a group of serial killers all of them playing Red John giving himself something to do    Killing          that's how Red John knew his list      that's why RJ is always one step ahead of Jane.. impossible to catch     

Just before that awful S06E8,there was a scene in which Bret Stiles was doing some weird religious ritual...............Why do you think they would show that scene? He also said that he will return? Strange words coming from a guy with terminal cancer don't you think? The question is what was the significance of that scene? What does that have to do with anything related to RJ? Your guess is as good as mine.

If you browse through The Mentalist's official facebook page and check the comments,you'll see what type of people are happy with the way the show has "progressed". Mostly mature women above the age of 35 who only watch the show because Patrick is cute and they want him to hookup with Lisbon. I think they mistook this show for a soap because this is Crime Drama!! It sickens me to see people say they are glad red john is over. 

Bret Stiles is alive and well -- and will make another appearance

Malcom McDowell didn't just get blown up to never be heard from again -- that doesn't happen to actors of his caliber