I think that without a doubt, RJ is Partridge.
Some may think that the idea of making the quirky, mostly creepy, crime scene investigator RJ is too expected. Well, are we not meant to feel in the moment when it comes to the show? How often do we hear of the head of a law enforcement agency is a serial killer? (the head of a ring of dirty cops? We most certainly hear that all of the time and Bertram is certainly the head of The Blake Association.) But how many times do we hear about the crime scene investigator, documentarian, etc being a sick, twisted, cynical, sociopath who enjoys being able to come back and marvel at their work in the public eye. After all, it is one thing for RJ to revisit the scene alone, but it is another when he gets to come back, document, photograph, and flat out glorify the "genius tactics" in the face of the law, quite literally!! Partridge as RJ means he photographs his work to forever memorialize it in his own ideal of his genius ways. So yeah, maybe it's cliche in the sense of television but it is by far the most plausible in real life. I find that more compelling than going out of the way to make some absurd story.
To continue with Bertram for a second, there is just NO WAY! I know people are saying, "Well why would he kill the bartender? Would The Blake Association fake that?" First and foremost, Bertram IS the head of The Blake Association. Do you all easily forget him quoting William Blake for whom the Association is named after? Also, this is why Bertram is so reckless at this point. He knows there is no way out of this situation, he is caught, RJ or not, they know he is a member. Killing the bartender was an easy out considering the bartender would mostly likely call the police and they would at least have a last sighting. The bartender was an expendable nobody. Also, he is still protected by the association whereas Smith is disposable to them...because he is just a low ranking member doing all he can to kiss some ass and work his way up, hence his involvement with Bertram and McAllister.
Now, McAllister is a strong probable for RJ. I could see him as a possible follower or admirer of RJ. I know there are many things that allude to him as RJ BUT I just do not see him fitting the role. He is not afraid of heights, he does not have short straight hair (I know some theories say, well Sophie is right but he may have been there a long time ago. Uhh...no!! Patrick told Rigsby and Van Pelt to look for a new client within the past 5 to 6 months. McAllister has always been rather balding). Also, if RJ was afraid of heights, he would not just rake his confidence to save Patrick on the roof of the church. I am only remotely afraid of heights but I would never do that. I can see McAllister as being a follower to the point that he becomes a decoy to confuse Patrick.
Partridge is perfect for RJ. How many times do we see false plots on The Mentalist where someone is not really dead (Does Hightower ring a bell?), and from there, let's discuss Partridge's death. One, he was the first suspect killed, since I also like the Lisbon is bugged theories, RJ knows he is being traced, so he needs to take himself out of the picture, so he does. He fakes his death. As we know, RJ is protected by The Blake Association so since Patrick was so concerned with Lisbon since she was attacked by RJ at that scene, he ignored examining the body. (Also Lisbon finds Partridge, he falls to the floor, Lisbon turns the other way to check out a room and is hit from behind where Partridge was...too convenient). So Partridge is off the map and free to move as he pleases. Of course Cho checks the body (only the arm NOT the head but I also believe he is working in private with Jane). Being a member of The Blake Association, RJ has all sorts of ins and can falsify any reports and documents. Also, lets go back a bit, when Lorelei was killed, Partridge specifically said it was an inside job. Why say that when it was still a RJ killing? I think he was caught in the moment and made a slip up. Also, not just be a professional and stick to the "it is another RJ killing" HOW MANY TIMES in the past has RJ killed his followers in the same regard? Did Partridge say that was an inside job then? NO! It was this time because it was personal. RJ felt betrayed by Lorelei's infatuation with Patrick. This made RJ feel that Patrick was better than him, it made him feel betrayed, and inferior (just as Patrick ALWAYS made Partridge feel at the crime scenes) and RJ just could not take that. He is egotistical, complicated and most importantly...consistent. Also, Partridge once claimed, "Oh I'm so excited to finally see a RJ crime scene!" Okay, if that does not SCREAM sociopath in of itself...he also says how many RJ scenes he has been to. Another slip up?
Yet ANOTHER Partridge slip up. When he's describing a RJ scene and he's explaining the smiley, he talks about it being clockwise, done in blood, with a rubber kitchen glove. Uhh...why would RJ ever leave or allude to his materials, let alone leave behind evidence that could possibly contain DNA? Partridge's annoyance at Patrick for ridiculing a new RJ style of of surprise. First seeing the body, THEN the smiley. RJ is an artist, indeed (as Patrick said) so RJ would want to alter his art, take new approaches. Partridge's excitement for encountering Jane at a crime scene, his mocking of Patrick's "psychic powers" (the same reason why RJ killed Patrick's wife and daughter), his agreeance and awe in Patrick's way of thinking while playing coy, his annoyance when Jane so quickly dismisses the possibility of an RJ crime scene. How much Partridge enjoys the ways of other killers, his almost euphoric state of admiration for the killing methods of others. Partridge's distaste of the ideal of murder as opposed to "the art of killing". The fact that Lorelei said Patrick and RJ should have been lifelong friends, the quirky way Patrick and Partridge play off of one another. How Partridge entices Patrick to debate on whether a crime scene is RJ or not, how he alludes and claims "Oh, this is not RJ" just to get Patrick to react, a favorite ability of RJ's. How Partridge satirically calls Patrick the RJ expert. Coy and playful, just like RJ.
Oh, and also? RJ's voice? CLEARLY it is the same pitch, tone, and quality as Partridge. The sly, ghoulish, well articulated crime scene investigator/Red John.