Questions that need to be answered:-

-Who is Red John?
-The "He Is Mar" clue.
-What happened at that house the night it blew up?
-How Red John knew Jane's list before he did?
-How did Red John kill Jane's happy memory?
-How was Red John always one step ahead of Patrick Jane?
-Why did Red John tell Patrick the poem of William Blake?
-Origins of the Blake Association.
-Why didn't Jane take Rosalind Harker's description of Red John into consideration before making the list?
-The Kirkland twins.
-Why did Red John kill Bret Partridge?
-What Brett Stiles meant when he said "I know more than you or Red John could ever know".
-Why the hell CBI Ron was in so many episodes?
-The freakin' pigeons!
-How Red John has so many accomplices that are willing to do anything for him?
-Red John's voice. As it couldn't have been the voice changer people use over the phone because his voice was exactly the same when he made his first physical appearance in the season 2 finale.
Feel free to let me know if I have missed any more in the comments below.
 


Agree?