Heller said there was a big clue in the first episode of season 6. I've read the most of the theories, most people think it is about the pigeons. But what if the clue is maybe the phone call? The way Red John and McAllister talk is always in a relaxing matter. The voice tone is only different, I tried to listen to the phone calls in episode 1 and 3, it sounded pretty much the same. And they both mention Patrick Jane always by his first name. 

I really like some of the theories on this site, they are really fun and thoroughly researched. I honestly think Heller is going to surprise us with many new plot twists in the last season. I just love this show!