"It’s always a difficult dance to balance those two things.  It got to a
point where some people were like, “We really love the show.  We really
love the Red John episodes, and then we love the stand-alone episodes
that don’t pertain to Red John, at all.  Is there a way that we can deal
with one completely, and then move forward from there?”  To be honest
with you, those decisions are not for me to make."
Read more at http://collider.com/simon-baker-bruno-heller-the-mentalist-interview/#c3OWoXCtEocf7MmX.99

What Heller is really saying is that Red John was nothing more than a plot device that attracted some viewers that normally would not be in for the murder of the of week drama. In other words, the clues did not matter when when it came to RED JOHN and to lesser degree did not matter to the murder of the week drama. The true fan base is with Baker and the supporting cast and the witty nature of the show. Since Jane was trap and unable to develop during his pursiut of the Red John many fns lost interest with the murder of the week and the lesser fan base became obsessed with Red John. The solution was to reboot the show only keeping what was essential. Lisbon and Jane. We will make the rest of the shit up as we go assuming we still have a fan base after we fucked it all up.
Love Bruno