This isn't necessarily a single accusation, but more of an analysis of each character in the final list of 7 and how he is possibly Red John and how he is also not. At this point, I'm not fully confident in one suspect so I will rank based on what we know about them. I apologize in advanced if this is too long, but thought I had some pretty good points and observations to bring up. Some of them may be a stretch but still something to ponder about.
Bret Stiles - He has helped Jane on two separate occasions: First time was when he told him the whereabouts of Kristina Frye and the second occasion when he orchestrated Lorelei's breakout. In season 2 when RJ meets PJ, he says something along the lines of "Kristina would want me to send you her love... she's very fond of you". RJ clearly knows that PJ cared about Kristina and was upset by her abduction. Later, Bret Stiles leads PJ to her, but it's too late for him; she is beyond his help. What if RJ knew getting PJ's hopes up but eventually crushing them would be a tantalizing way to mess with PJ's mind? Similarly with Lorelei, he knew Lorelei wasn't going to talk (except for letting slip about shaking hands, which he apparently was furious about), and deliberately let her get released? Not to mention Lorelei expected it would be him to break out her out and we know Bret Stiles is definitely one of the people capable of this feat.
On the flip side, there are a few hints that suggest he is not Red John. One fact is that Rosalind Harker describes RJ to have straight, short hair and Bret Stiles seems to be more of a balding type (granted, she may have felt the back of his head). In addition though, she felt his face and surely would've felt the wrinkles and deduce he was pretty old. Is it likely she fell intimate with someone that much older than her? This is more of conjecture than factual reasoning, but something to consider nonetheless. Also, his voice doesn't sound remotely close to RJ's voice in the season 2 finale (again, he may be good at changing voices). The last detail is that Stiles seems to have a "friendly" relation with Jane; they talk quite casually without much sign of hostility and he also voices his concerns about Jane being caught for his involvement in Lorelei's escape.
Gale Bertram - He was on the original list of 4 suspects back in season 3 along with O'Laughlin, Ardiles, and Shettrick. What if RJ figured out Jane's trap because he knew the 2 locations (Bertram's and O'Laughlin's) contradicted each other? Why else would he hire the assassin to go through the trouble of using a rope to traverse to a room when she could have simply walked into O'Laughlin's right away? Perhaps it was a subtle teaser to Jane as a sign of "you almost got me, but not quite" and throw Jane off the trail. Not to mention he used the word "rope" when he says "you reached the end of the rope" as opposed to'line' ("you reached the end of the line" is far more common). This seems to be one feasible way of staying ahead of Jane; he provides Jane an answer that makes him THINK he's onto RJ when in fact RJ's been manipulating and pulling the strings. Lets also not forget that he's seen collaborating with Bob Kirkland (who definitely has a strong connection to RJ) after he interrogates Lisbon about Lorelei. A more minor detail is that poker is seen extensively throughout the series. Bertram is an avid poker player and we also get a rare closeup of his hands (you have to use your hands to play poker!). He and Brett Partridge are the only two characters on this list where we get a somewhat zoomed-in view on their hands (part of Harker's description on RJ).
In terms of evidence that it's not him, he has a similar one to Bret Stiles; balding and not much hair, and also the voice (again, this is arguable obviously). He also receives help from Jane (poker) and doesn't seem too ashamed about it. He's also keen to keep Jane in prison (when he tells Ardiles to try and stop Jane from bailing) and we know for a fact Red John enjoys Patrick Jane chasing him and will in a way help Jane get back on trail (killing Bosco and his team back in season 2 for instance)
Reede Smith - This is probably the one person on the list that I cannot connect to Red John. If anyone has any theories on him being RJ, I would be intrigued to hear it.
Ray Haffner - All the reasons that he is RJ have been stated repeatedly so I won't post them (Red Barn connection, link to Visualize, high ranking CBI position, etc).
Why I think it's not Haffner: RJ knows Jane and Lisbon are inseparable. Haffner doesn't seem to, he keeps trying to prod Lisbon to come with him over Jane. Haffner has also been played by Jane, something that hasn't really happened to RJ so far. Haffner is also a former football player (award in his office). Being a football player, you would think he would be quite built, but Rosalid describes RJ as "not muscular". He is also supposedly leaving CBI, and look at the other suspects that were "leaving" who's been eliminated (virgil Mineli to Hawaii and Walter Mashburn to Europe anyone?) There also doesn't seem too much personal animosity between these two.
Bob Kirkland - He provides Lisbon with details about the case with Lorelei's sister, which was a dead giveaway in letting PJ try to get Lorelei to cooperate. Doesn't he know that leaking that information would risk Lorelei revealing to Jane who RJ is? Again, this goes back to my theory how RJ purposely gives information (misleading and not always quite enough) to trick Jane into thinking he's ahead.
Here's why I don't think it's Bob: RJ predicted (or rather knew) PJ's 7 suspects far before Bob broke into Jane's room and did an analysis of his findings. It seems far more likely that Kirkland is an accomplice and he merely sent him as a way to confirm his suspicions. He always states along the lines of "you don't know me, but I know you". Wouldn't this indicate he's not Red John (of course, one could argue depending on his/her interpretation but I personally think this was meant in the way that Patrick does not him because he's not Red John or someone else he's met before).
Thomas McAllister - The only connection I have is that he's a Sheriff and we know that Red John's association Orville Tanner had a son who was a sheriff himself: Sheriff Hardy back from the season 1 finale. A couple people also hypothesized that he lost on purpose in rock-paper-scissors to give Jane a false sense of security. Apparently, Bruno Heller also stated that RJ will be a "where's Waldo" type and 1 appearance does fit this criteria (I do not have a citation for this, however, someone confirm please?)
Why not him? This sort of contradicts what I said just now but I feel like 1 appearance isn't really enough to constitute the final villain. We also know very few details about him and I think the purpose of the show is to try and utilize/connect as many details we know about the suspects and make a logical guess.
Brett Partridge - I have no additional insights to the ones already been stated constantly. There are quite a lot of theories that suggest it's him.
Why I think it's not him? Way too obvious, seems like a Red Herring, and since when has a really obvious suspect ended up being the culprit in any of the episodes (filler and no-filler).
Again, I have no clear suspect but if I were to rank in terms of likeliness, it would be:
Unlikely: Reede Smith, Thomas McAllister
Possible: Bob Kirkland, Bret Stiles, Ray Haffner
Likely: Gale Bertram, Brett Partridge
