So my theory actually ignores most of the evidence, because as far as I'm concerned at this point the suspects must be able to fit most of the evidence given or they wouldn't really be suspects to Jane. 

The events of season 3 seem to solidify Red John as a man of psychic ability, and again we have events in season 5 that seem to corroborate that fact.  However, Jane constantly proves that Red John uses Patricks methods of mental deduction.  In order to enter Jane's mind to get the list of the 5 suspects revealed at the end of season 5 he seeks out Jane's old therapist.

As such the events of season 3, Hightowers frame up, and Jane's resulting trap set up an event where Red John MUST be in the suspect list at the end of the season.  Because Red John knowing its a trap STILL has to accept Jane's terms and send someone in.  But in order to plan accordingly and be safe he has to take in all the information he has.  As such he cannot be prepared to enter bertrams room, AND repel down to o'laughlin's room UNLESS he is privy to both room numbers and as such the trap itself. 

Lastly when confronted about murder Bertram is incredibly cool about it, he doesnt question Patrick judgment but merely defends himself (reminiscent of the very first episode where jane points out that an innocent man would have punched him by now).  He during that conversation uses the phrase "at the end of his rope" which i beleive is a tactic to elicit Jane's memory of the trap knowing that Jane is about to spring his plan.  This mentioning of rope is inevitably what leads Jane to focus on o'loughlin and divert his attention to the other "Red John" in the room, and is a common practice amongst proclaimed "psychics"