A few things to consider:

1. Bret Partridge is dead. For those who think that he is still alive, and mostly likely Red John, you're wrong. He looked like a prime candidate, but this is the Mentalist. No one saw Craig O'Laughlin being a Red John disciple, but it happened. Partridge is down, with six likely suspects remaining. Which leads me to suspect Gale Bertram even more.

Bertram is the director, and can access anything he needs to know. A few reasons I suspect him...

1. In the season 3 finale, when Jane tells him of the meeting with Hightower at the mall, Bertram at first hesitates, and then agrees. As soon as Jane leaves his office, Bertram picks up the phone and calls someone (likely Timothy Carter).

2. He mentions to Jane in the same episode "reaching the end of your rope" leading on to believe he knew the whole setup was a trap. O'Laughlin tells Bertram he was told Hightower would be in room 605, Bertram was told 505. Immediately realizing it's a trap, Bertram sets up one of his own.

3. Back to the present: When Jane and Lisbon encounter Bertram in "The Desert Rose" He is angry about the previous case, and presents two options: agree to a suspension, or take a case far away. Really? Those are the only two options? Bertram knows they'll take the second, gets Partridge out to the desert to meet them, and everything plays out how he wants.

4. Bertram also says "Jane's getting close, or at least thinks he is. Everyone's talking about it." I'm not so sure about this claim; Lisbon and Jane would've heard if people were talking about how close he was. I think this was a mistake made by Bertram, and he acts flustered, which doesn't help. I remember back to when Lorelei shot Jason Lennon, she says to Patrick "Red John's not perfect, he makes mistakes." I think this was another.

5. Lastly I look back to the ending of "The Desert Rose." Lisbon gets a lead, and discovers Partridge is at the scene. This makes sense for anyone who could be Red John. They leave their cell phone at a location, because they know it's bugged, and go to the scene of the crime without it. It would throw Lisbon, who is tracking, and it would be a perfect alibi. Plus why would they need a cell? They know Lisbon will have hers. So Red John arrives, wounds Partridge to the point of death, knowing he will only say "Tyger Tyger" before dying. Lisbon arrives, finds Partridge, and then she is knocked unconscious, while Red John calls Jane from Lisbon's cell. The most likely suspect is Bertram for this, continuing from the reasoning above, and the reason I think he didn't kill Lisbon, was because he knows she can still be of use.

Please let me know what you think. There are a lot of other motives for Bertram, but these seemed to be the biggest.