For those who think it's Bertram, I just rediscovered a really important clue that shows he can't be Red John.
We now know that Red John has a burning desire to befriend Patrick. He wants to be friends with him so badly that he's willing to expose himself and put himself out in the open for Patrick.
Red John + Patrick have been playing a game of cat and mouse for years, and Red John enjoys it. We know that Red John really cares about Jane.
In the season 4 premiere, Bertram tries to get the assistant DA to ask for Jane's bail for the murder of Timothy Carter to be extremely high, and also to ask for Jane to serve the longest/harshest sentence that the law could allow.
Red John, as we've seen, does everything in his power to keep Jane in their game of cat and mouse, such as killing Bosco and his team so that Lisbon's team gets the RJ case back.
So if Bertram is RJ, then why would he try to keep Patrick imprisoned for as long as possible?
Thus, it's very unlikely that Bertram is Red John. If he were Red John, he would have been a heavy advocate for Jane's release from prison, instead of trying to pull strings to keep him imprisoned for the longest sentence possible.
