Bruno Heller, on the first episode of season 6: "There is a clue buried in that final sequence that will pay off big time in the finale of the Red John story. A very big clue. No one will get it from the clue as it is laid out in the episode, but it will pay off later."

Now does anybody know what the hell is this man referring to? He hasn't talked again about this "very big clue" (he hasn't explained ANYTHING for that matter). 

Asuming that Heller was telling the truth and there's indeed a big clue hidden in the final scene of this episode, the only thing that I can think of is the room full of pidgeons. When Lisbon opens the door of that room, a pidgeon goes out flying, so here's my question: if Red John is McAllister, and McAllister has a pidgeon phobia, is it really posible that he was in the shadows waiting to get Lisbon with a pidgeon flouting around? Doesn't make sense at all.

I really hope this is a big trick and everything will be later well explained, And it may be wishful thinking and I may be delusional, but my money is still on Partidge. Yes, he is "dead", but McAllister was also "dead" and there he went walking around churches and getting scared by pidgeons, so I don't think we can rule out this theory that easily.