Bertram taunts Jane and Lisbon about getting close to Red John
and says coyly, "I am many things to many people." That exchange
certainly casts a lot of suspicion on Bertram.
Heller: Yes,
it does. He's a very suspicious character, and those suspicions are not
without foundation. [But] they're not necessarily the foundation that we
think they are. One of the things that is going to be revealed in these
next few episodes is that there is a whole lot more going wrong in
California law enforcement than simply Red John. And Bertram is both a
prime suspect as Red John, but also deeply involved in that other plot.

http://www.tvguide.com/News/Mentalist-Bruno-Heller-Season-6-Premiere-1071429.aspx

Important points:

1. Red John knows about the phone bugs. Jane has no doubt about this and
says so, so why should we as viewers have any doubt that RJ knows about
the phone bugs. If he sets a trap for Lisbon as part of his killing of
Partridge, he would obviously leave his bugged phone at a different
location. The location of the bugged phones on Lisbon's computer screen is
therefore not a clue worth paying attention to.

2. Bertrum's weirdness at the beginning of this episode can be ignored. Heller is not so stupid to feed us obvious clues like this. As usual, this is just classic narrative spicing. Each episode he will likely make a different suspect a little more suspicious. Ignore.

3. Partridge may not be dead, but he is not the person who attacked Lisbon. The door to the bathroom opened while Partridge was on the ground bound with packing fasteners. Whomever attacked Lisbon was either RJ himself or an accomplice - but clearly not Partridge. I would very highly consider Partridge dead, and I see no reason for Heller to be so deceitful about this. In the post-mortem interview with Heller, he clearly states that RJ needed BP dead at this stage of affairs to complete his grand plans. We should try to understand why this is, rather than consider that BP faked death in an elaborate 2 man operation.

4. RJ holds the bloody blade used to cut BP in his left hand as he wipes blood from it with his right hand, and then smears the smiley face on Lisbon with his right hand (or so it appears). This may be a clue.

5. The room with the 7 pidgeons in it, and with 1 flying out -- this is a clever cinematic device, but if this is indeed the "clue" that Heller refers to, it is weak sauce to say the least. In fact it does nothing but tell us what we already know and are just finding out -- that there are 7 suspects, and now less 1. Are we meant to conclude that RJ is planning a really cool murder scene - so he lures BP to a condemned house and to kill him, and also goes to the effort to plant 7 birds in a room to be a cool metaphor for the 7 suspects in the assumption that Lisbon (or later Jane) opens that room and counts the birds and thinks how clever RJ is?? ... to me, this is just clever (or perhaps wanky) directing by Heller as a 'wink' at the audience. It surely holds no significance.

6. Not really a major point to think about, but it's lucky that right as L is about to open the bathroom door, BP makes a groan in the closet so that she goes there instead. Had she opened the door she would have seen RJ and would have been killed by him (no way he can let her live then), and then the whole Partridge element of the plan would have been wasted. Lucky that BP groans? I guess so.

7. BP saying "tyger tyger". Was he told to say that? Not possible. Most likely this poem was recited to him by RJ as he was killing, binding, and forcing him in the closet. So it is the only clue BP can think of to tell Lisbon as his dying utterance. We must assume BP never sees RJ, as RJ would never let this happen or he could just i.d. him to Lisbon as he dies. RJ must have planned for BP to be able to say a few final words to L and wanted to plant the "tyger" clue deliberately.

So i am of the mindset that Partridge is dead and that this was not a trick of his. If you watch the scene closely brett partridge is on the floor face up telling lisbon " tyger tyger" when the door behind lisbon opens. So it cant be partridge opening the door because he is on the floor. It was red john who openened the door and just hides behind the door as it opens. And you can clearly see that lisbon is pulled from behind, not from the bottom as many suggest.

Partridge is not realy a strong man so i doubt he could have pulled lisbon and knocked her out while he was laying on the floor. Lisbon is clearly pulled from behind, you can clearly see the angle she moves.

And red john could have easily left his phone at some other place because he knew they were bugged thats why no other signal appeared except the one for partridge.

I most surely think Partridge is dead, i think he is really overestimated. He is just a weird lab geek who is creepy and likes seing dead bodies.

Okay after reading a few other theories I believe Kirkland and Stiles is RJ and POSSIBLY Bertram. It seems far fetched but I just think it might.

I am positive that the words written in blood when Jared Renfrew was murdered is "He is many" written by Renfrew.

Most refer to Patrick Jane as Jane. Red John, Kirkland and Bret Stiles are the only alive ones remaining that call him Patrick. 

When Patrick Jane first meets Bob Kirkland, Bob claims that he knows Patrick - Patrick doesn't seem to know him though.
Even on Patrick's first day, Kirkland was after him. He got a woman to call Bertram to inform him that Patrick was a mental patient and had the potential to work for RJ or even be RJ.
He hired 2 Homeland Security officers to break into PJ's attic to get a replica of Jane's pin board and other theories/leads. This data could have EASILY allowed Kirkland to shortlist the same suspects that Jane got.
He killed RJ's friend in hospital with the poisonous injection but DID NOT ASK HIM WHO RED JOHN WAS (which seems like an extremely obvious question to ask unless you know who is).
Kirkland said if he were in this situation he would want a "friend" to do this for him - accomplices are often referred to as "friends" of RJ

Visualize seem to be at the root of everything - between the red barn smiley face, Lorilei saying that she has reached her full "reality" after the death of her sister (that nothing can hurt her now), and the extreme hypnotic devotion of the group to Visualize.
All of RJ's followers are completely devoted to him. They would rather kill themselves than be taken alive by CBI or other police forces.

In Season 6 ep. 1 Bertram is just out of character. 
He told Jane and Lisbon that there were whispers that Jane "was getting close. At least he thought he was." then got jumpy and kinda flustered. Wouldn't Lisbon and Jane heard people saying stuff around the office? Bertram's smart remark about Jane thinking he was getting close seemed to be a rare mistake of RJ. 
Also early in an earlier season Bertram recited a poem written by the same man that wrote "Tyger! Tyger!" that RJ recited to Jane after rescuing him. This was extremely out of character for Bertram. He has never in any prior episode expressed interest in poetry nor literacy in general.

As I said at the beginning: unlikely but possible.
Anyways let me know what you think please!

I think we may have been given another clue about Red John during the final 10 minutes of the show.  Lisbon was looking at a computer display with a map of California and each of the cell phones she had tapped (P-Partridge, B-Bertram, H- Hafner, M-McCallister, K-Kirkland, and S1 and S2 for Smith and Styles).

If we the map was correct and each of the suspects actually had their cell phones, then we can probably rule out a few folks.  Kirkland was in LA, and Styles and Smith were both in the San Francisco area.  Even McCallister appeared to be about 45 minutes away from the house where Partridge was killed.  The two suspects who appeared to be near the home were Bertram and Hafner.

Since the show went out of it's way to point the finger at Bertram, I think Hafner was the one most likely to be at the house ... if it was, in fact, Red John and not one of his accomplices.