Some fairly unnoticed points that need to be explained:
1. Why is Haffner so interested in the Red John case? He referred to a client who's interested in the case. Logically speaking there are only two possibilities, First, he is Red John and there is no client. He is not Red John and there is a client. But who is the client? Visualize? Stiles doesn't seem to be interested in the Red John case, why would Visualize be? Is the client Red John himself?
2. Of what nature was Kirkland's relationship with Bertram? They seemed to be close. Apparently Bertram is a member of the Tygers, and apparently Kirkland was after the Tygers. So was Bertram playing a role and fooled Kirkland? If that's the case why would the Tygers let Kirkland get close to Jane and the Red John case? Or was it the other way around. Or maybe Kirkland is a high-level member of the Tygers about whom only Bertram knows, and they faked Kirkland's death, Which could make it possible he is Red John.
3. How did Stiles know the whereabouts of Kristina Frye?
4. Is Rosalind trustworthy? If she is, why didn't Jane take her description
into account? If he forgot to do that then he's incompetent; if he
didn't and the producers did, then they're incompetent. If she's not
trustworthy, why did Jane ask her whether Timothy Carter was Red John or
not?
5. Is Alexas Shultz a Tyger member? If she was then why would she work for Kirkland? Would that confirm Kirkland was a high-level Tyger member? Or possibly Red John himself? If he is Red John why would he kidnap men from Jane's fake list and ask them if they're Red John?!
6. Why didn't Jane set a trap when he knew Red John was going to kill James Panzer(aka the SJK)?
And many other unanswered questions.