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