Red John has been McAllister this whole time. Big clue is that Red John slices up his victims. He must be a doctor with the knowledge he has of anatomy. However, he could be an avid hunter, and Thomas McAllister is an avid hunter.
There is speculation about other people being Red John. These theories aren't exactly true, because it was Thomas McAllister. In order for those theories to be true, McAllister would have to be a patsy or he took it upon himself to become acquainted with Red John to cover for someone he loves or he wants to protect (from Jane).
This person would need a story that is troubled. Rigsby had a tough upbringing, but Lisbon has had an even tougher upbringing. Her unnamed brother could be Ray Haffner. Her father could have been killed by her brother, since her father almost killed one of her brothers. Lisbon says about her father that "he almost killed" all of us. Her brother could be upset about his mother being killed in a car accident by a drunk driver (he feels cheated). His father beats him or his younger brother nearly to death. He then hides after killing his father in "self defense" on the visualize farm. Lisbon was raised in Chicago, but she became a police officer in San Diego. Visualize is a possible access to this better life through its farms. Her or he brother go to college get degrees, and they become police. Her dad was a firefighter, so the children probably got some scholarship. Anyone of them could have made it.
Possibly Ray Haffner fakes McAllister's death, and his own. He sets up a meeting with Jane to reveal said coverup. The coverup is realized, and the other bodies weren't investigated. Red John could make that happen; McAllister almost got away with it. As everybody is looking at McAllister, they realize he is Red John. Truthfully, he probably did work with Red John or killed as Red John. I believe he did the Red John murders that the show has revealed, but the other murders could have been someone else. The killings before 2000 could be someone else. Orval Tanner could be McAllister's friend; Tanner is the reason everyone thinks Red John is old. Orval Tanner dubs Smiley Face killer as Red John, and from there Red John is a notorious killer. The original smiley face killer is still a mystery.