Having read the synopsis for episode 6.21 where Jane finally faces the consequences for killing RJ, wouldn't it be interesting if those consequences were from killing Timothy Carter, NOT McAllister.
What I mean by that is this:
Most hard core fans who watched the show from the beginning seem to be in agreement that Timothy Carter made a great Red John and had the series ended in the mall with Jane killing Carter, a lot of questions would have remained unanswered, but it still would have made sense since Carter fit all the clues to that point.
Conversely, those same fans seem to be in agreement that revealing McAllister as the real Red John was lame at best because the same questions still were unanswered and he fit very few of the clues from earlier seasons. It simply didn't make sense on any level.
So what if Jane was in a coma ... not from the explosion in season 6 but in rather in a coma from some sort of beatdown (or something equally traumatic) that happened when he went into custody after the mall scene at the end of season 3 before his absurd acquittal in the first episode of season 4?
If that were the case it could plausibly explain the idiotic and unrealistic events that happened every now and then in the series from seasons 4 to 6, since the longer Jane is in a coma the more fantasy like his reality becomes.
So in essence what has happened between season 4 episode 1 and now has been in Jane's dream world as he becomes more out of touch with reality with the passing of time. Maybe Carter was the real RJ, maybe not. If he wasn't, then maybe (and I'm probably giving Heller way too much creative credit here), Jane has been subconsciously putting the pieces together while in his coma and the clues that we see as totally unbelievable in the real world are just symbolic in meaning.
The real meanings and how they tie everything together will be revealed when Jane finally has his real day in court for the crime he committed at the end of season 3.
I realize this is hail Mary theory in hopes that the series doesn't crash and burn in total suckdom. I really don't care who RJ is (even it was McAllister) as long as it's explained and actually fits the clues given since the beginning.
Anyway, hope that made sense.