I'm just throwing this out there, obviously, I haven't had time to think all the "what ifs" through.

But what if Red John is some sort of invented persona by the Tiger Tiger Conspiracy?  Kirkland said he suspected it existed so that they could "get away with murder"?  What if they cover their tracks by making it look like a serial killer, aka RJ, did them?  What if they killed Patrick's family so that they could lure him in, having him as an official expert on the case to track a person that technically doesn't exist in order to cover their tracks?  There's a person posing as Roy, Jay, RJ, etc., but the conspiracy uses RJ to cover their tracks for their own sinister purposes.  But they keep Jane and Lisbon alive because they need a team to track RJ, making it look as if they're really interested in catching this sinister individual.

Having said that, I'm personally leaning toward McAllister for RJ, but I'm just mulling over this possibility, too.