I think that Brett Partidge was the Red John killer (the individual who actually did the killing) and was either the son of or connected with Bret Stiles since a very young age (as he was the individual on the Visual farm we learned about last season). Now, Stiles would want to protect his son/apprentice (whatever he is) so he used his influence with the church and his money to buy off FBI agents, recruit church members, and put people in positions of power to help protect Partridge (Red John's disciples). These people include the likes of Gale Bertram, McAllister, and the other suspects. However, despite their promises to Stiles to protect Red John (Stiles may have helped them get there positions in law enforcement, etc.), as Jane narrows down the list to 7 suspects they realize that their plan has become too risky and they may all be implicated. As a result, they decide to kill off Partridge and the people who have information that could incriminate their entire group. So, they lured Partridge to the house with a promise he could kill Lisbon and, instead, killed him. Then they had one of them call Jane (using the voice changer Partridge used for his Red John voice) and say the line "Lisbon can't come to the phone right now" (thinking that they've covered up all the evidence and are sending Jane on a wild goose chase for a serial killer who is already dead). This would explain why "Red John" didn't kill Lisbon, because it was Bertram and Haffner and the others...all people who like and respect her.

Of course this is all speculation...but it does explain the "He is mar" clue as "He is many". It could also explain the conversation we just saw in S6E2 where McAllister and Agent Reede are talking to Bertram and ask him "how much Jane knows"...hinting to the fact that they're all involved somehow. Bruno Heller has also said that following the conclusion of the Red John storyline, the show will have another direction to go in (and the conflict with Stiles and Visualize could be that direction, as Jane didn't get his chance to exact revenge on Partridge/RJ so he will want to exact revenge on those who enabled him).

Hey guys, i'm not gonna escribe a pretty large text saying what everyone here has already said.
I will leave you with an image that i've done:

http://i.imgur.com/6Ez7I0R.jpg

I've found that old lady feeding the pigeons REALLY weird when i saw this ep. Also, remember the pigeons in the first ep? Then i started thinking and got to this. 
Really don't know if this is relevant at all, just a thing that i wanted to share with you guys!
Thanks!

pigeon  [Pi]-John 3,14 JOHN

1 JOHN 3,14
We know that we have passed from death unto life, because we love the brethren. He that loveth not his brother abideth in death.

Something doesn't make sense with the death of Partridge. A call comes to Lisbon, saying someone is in distress. She sees that Partridge is there, goes there and when she gets there he is still alive. He dies after saying two words. Then, RJ puts Lisbon out and doesn't kill her. Questions are:

1- Why did RJ need to kill Partridge? 
2- Why was he still alive when Lisbon get there? 
3- What was the point of luring Lisbon into a trap if she wasnt gonna get killed? What did RJ accomplish here? 

 Since I don't want Partridge being dead, I'd like to think that Partridge himself set the trap to remove suspicion on him. The best way of doing that is faking his death.

I appreciate every single opinion. Please feel free to share what you think.

Just a theory, but what if Brett Partridge has a twin brother? (fearful symmetry). Possibly.

The man "Partridge" is dead, but now Brett Partridge is just Red John now...to take himself out of the suspect list
to now pursue the murders as Red John without being in or around the CBI anymore?

After watching episode 2 of season six, I heavily suspect Partridge. He was hardly mentioned after his "death". Im almost 100% RJ's phobia has to do with pidgeons after seeing how Jane watched them. The description we got can't be trusted. RJ would know if she was recording it, he wouldnt do something to stupid without thinking. So basicslly take the description and forget about it. We all got distracted by the whistling, but that was meant to be misleading. There was a reason there wasn't anything about Partridge, RJ wouldnt give hints about who he truly is. 

But I could easily be wrong.

Thought i'd just throw this out their, as a different perspective to those already offered. Bruno Heller has come out and said that Brett Partridge is dead. I believe Red John is a bit like Jekyll and Hyde, a psychopath that is excellent at hiding his bad deeds. The Jekyll side usually diminishes over time. In the case of Brett Partridge most people thought he could be red john from the very start. (Heller stated Red john was in it from the start, same as Brett Partridge). During the video read by Lorelei one of the lines was "I will start killing again". To do this Red John needs to regain control, Red John is aware of how close Patrick is to finding him, so he pretends to die. Therefore regaining the control his craves. This means killing his Jekyll (Brett Partridge) so all is left is his Hyde (Red John) for a final killing spree. Hence Bruno Heller saying Brett Partridge is dead, which throws off Patrick (or so Red John hopes).