I have posted this theory already [and so have a few others now] so it's hardly new, but I notice there are still many posting about their confusion over whether RJ is dead or alive.  Understandable!  

But just wanted to say that I felt much better about the first eight episodes and the show in general after I realized that seeing the situation in either black [RJ's dead] or white [RJ's alive] -- is the problem, it causes confusion and disappointment, because we have been led to believe that McAllister is Red John, but we know that this defies logic, as well as many clues.

Thus, a new answer is needed to make both arguments work -- and that is that RJ is BOTH dead and alive.

The man who killed Jane's family IS DEAD [McAllister, an RJ henchman] -- thus Jane's killing of McAllister will be justified, and yet the person who ordered this killing is ALIVE [RJ, the mastermind], and so the show continues, as we do not know who this is quite yet.  The reason we do not have any resolution to clues is because only RJ the mastermind holds those. 

RJ is one brain with many tentacles. This really is the ONLY WAY everything works together and it all makes sense.  Think about any good mystery you've ever seen....getting toward the heart of it, it's always the henchman you find first.  Any leader has foot soldiers.  We are only mid-season, so get ready.