Macalister is not Red John reason #1748385
(I re-wrote it and added some)

Why on earth would Macalister show up at Patricks house knowing darn tootin well what was going on and submissively let it happen, then set off a bomb that would f him up in the process i assume right ?
Then let Patrick live; fake his own death, just to appear a day later to frame Bertram as himself and kill Patrick?
He coulda just killed everyone Jane's house and handled it there instead of getting surrogates and dragging bodies and all that noise. Makes no logical sense.
Red John could of killed Patrick a kajillion times in six seasons but he didn't. He choses to let patrick know he has this "list", kills Partridge, hires an outsider to un shadily put a bug on Cho's desk, kills her, then goes to a meeting at Janes house and blows it up and only kills Styles and Haffner and lets Patrick live. Then it was finally time to kill Jane ONE DAY later ! Why? "The game is over and i won". Oh, really did you? Just because he walked out with a gun its game over? Lol. Seriously laugh out loud. He coulda pulled out a gun on top of that roof at GVP and Rigsby's wedding !

Also Jane said the scene at his house was theatre, and what ever seemed to be true then the OPPOSITE was true.
Well the opposite of what happened would be that Red John was not even on the list.
Macalister faking his death wasn't the opposite of what happened at all.

And what about the infamous gunshot? A concussion bomb is a grenade. It goes boom! We all heard a gunshot then the house blew up but we missed what happened in between those two events.
Patrick had a flashback at the hospital. His flashback ended right before the gunshot. If it was simple amnesia from the bomb them he woulda forgot a whole lot more than just moments before the boom.
*I think this PROVES that there was mind control and hypnotism going on at his house. By whom? Most likely the real Red John. The guy/girl who made Kristina Freye a mute . The guy who makes his followers love him and die for him with a smile on their faces. Charles Manson'ish in so many ways.
The BA and their members exhibit hardly any similarities to Red John followers. Blake Association is just normal cops and law enforcement that are doing favors in a mafia like way for a boss that they have never met or even know his name. And they don't have crazy eyes like Sheriff Hardy, Bosco's secretary, Rosaline Harker (jk), Todd Johnson, the lady that stole the baby, and the lady in the church. Lorelie Martins is different . She was more than a simple pawn. A high ranking night in shining leather armor.

The reason why Jane seems off in episodes 1-8 is even more proof. Hardly caring that Red John guessed the list, telling Lisbon fatal secrets, not caring that CBI was shut down and just being totally apathetic in every way.
Jane is not a "new man".
He has not gotten over anything or quieted any dark spirits that haunt him. He still sports that wedding ring. He did not just join CBI's and his nemesis, the FBI because he was bored . He needs them. Jane uses people on the regular.
He has a plan, and watching it unfold will be like 10,000 dominoes all falling down one by one .
Check mate .