RJ's characteristics in total...simply do not match up, and I've long though RJ was two different people [or many].

RJ No. 1 is refined, loves Bach, wears fine suits, sips tea the right way, appreciates beauty and women [Harker, Lorelei] is clearly educated, clever, manipulative, with extensive knowledge of many things, including surveillance, as well as hypnosis.  This RJ is persuasive, and as such must be a lover to have such a devoted female following, but he is also a power hungry egomaniac psychopath who believes he is a god amongst others.  However, I doubt this RJ would get his hands too dirty.  He has minions, for this RJ is the MIND, the CREATOR, the ARCHITECT...

RJ No. 2 is not refined, and has the ability to kill in a way that would make anyone else sick.  This is the small time worker, though someone on a power trip, too, albeit on a lower lever.  He has the ability enough to carry out his deeds with his own hands, and knows very well what it is he specifically knows, but is not broadminded enough to resist being manipulated by someone smarter.  This is someone, who under the right influence [or hypnosis] could be manipulated to do to people what he has long done to animals.  This is the HUNTER, the WORKER, the STOOL PIGEON...

So, did Patrick Jane fulfill his mission and kill the man who killed his family?  

I THINK YES.  I think McAllister was the man who did that deed, physically, and as such, it was appropriate for Season Six, ep. 8 to have happened [even if I still don't like the WAY it happened]

McAllister was RJ No. 2

THIS IS THE ONLY WAY SEASON SIX CAN BE EXPLAINED as having been LEGIT and would make sense for why things were so confusing....Jane knew that McAllister was the one, but also that he was RJ No. 1's decoy

RJ No. 1 sent McAllister to kill Jane and frame Bertram because HE KNEW Jane would be ahead of McAllister.  RJ knew he could count on Jane to get rid of McAllister for him in the name of revenge.  And in RJ's sick, warped mind, he probably thought that he was giving Jane a gift, an emotional catharsis, handing over to Jane the man who killed his family. 

ANOTHER STOOL PIGEON:  HAIBACH -- it was RJ who killed LaRoche and Ardiles, just like he killed Wainwright and Bosco...NO WAY small timer Haibach masterminded an elaborate surveillance plot....RJ was using Haibach to try and take out Grace and Wayne...

SO......Jane is still hunting, waiting patiently and playing the game...because...

The question that remains:  WHO IS RED JOHN No. 1....?

BRET STILES
RAY HAFFNER
MICHAEL KIRKLAND
KRISTINA FRYE
CBI RON
VIRGIL MINELLI
WALTER MASHBURN
GRACE VAN PELT

What annoys me about Thomas McAllister being red john is that the same actor (Xander Berkeley) acted as a character with a secret organisation already in nikita. 

Am I the only crazy one who has ever fantasized about Jane's wife, Angela, being alive and somehow involved with Red John? lol  

Obviously this is purely fantasy, but sometimes I like to think about alternative options. Everything is better than a scared old man begging for his life and terrified of pigeons. 

I think it would have been cool if there was something shady about the wife. :D

 it is quite simple if you remember how Jane operates and the idea of the show has been and is ...at least so far true to.

Jane tried to lure RJ out but going on his own and separating from the CBI in Vegas. He is betting that the actual RJ will miss his playful rival and reveal himself now that Jane is completely out of the picture. That is overly simplified but it is the idea of how Jane operates. McAllister could not have been RJ for so many reasons, such as he was not afraid of heights. Remember how secretively Jane is. Just like RJ. Go figure......

People kept on saying that they dragged the Red John storyline on long enough, but for them to introduce another love interest in Patrick life is quite pathetic, after the season 6 finale, even though it was horrific, puts an end to wether or not he will get together with Lisbon . 

One thing I don't understand is that Heller said that "Up until now if you're comparing it to Moby Dick, which is one of the analogies I used to describe the length of the chase, next season the whale has been sighted and they're in the small boats and chasing the whale", isn't that what he said about Red John at the start of season 6.

Bruno Heller if your going to make season 7 about Patrick and Lisbon's love life, just give up now