I tend to think practically. If Jane was John, then it would ruin a lot of the series. It would put Jane beyond redemption. Who would ever buy merchandise and watch old episodes if they knew that they were just watching a crazy murderer who was the star of the show?
I absolutely love the theories that accuse Patrick Jane, though. Playing off of everyone's hopes/fears, I actually expect that there will be an episode in which Red John tries to convince Jane that he is, in fact, Red John. And Jane will probably be forced to seriously consider this possibility.
I don't recall specifics, but I remember two episodes in particular where people were held in high suspicion simply for being obsessed with RJ. It is a gaping hole in the show that Jane has never yet been really accused of this.
I think it's important to keep things in perspective too. I know we all care about Patrick, and we want to know about Red. But in this series alone we were faced with a character who killed an entire village of people! That has to be worse than Red John, right? If Red has to be portrayed as the true villain in the show, we're probably in for some major shenanigans yet.
Just thought I'd pitch in my two cents. :)
