Please note, that I don't think it's Jane, and posting it on Jane's theory on purpose, to prove all of you wrong.

Reasons why Jane isn't Red John:

I will start with easy ones that prove almost nothing

1) He shook Red Johns hand. Since he can't shake his own hand - it's not him. Anyone would respond -   Jane might have a split personality, and RJ made Lorelei tell Jane that it's someone he shook hands with to throw him off the trail, or start another sick game of hide and seek. Possible... Unlikely but possible.

2) Kirkland steals Jane's notes. He might be Red John, might be one of his pawns or a secret investigator. If we assume he is either Red John or his pawn (Because the last one is very unlikely) then comes up the question, if Red John is Jane, why would he need his notes? Doesn't he posses all the memories Jane has?
In case you tell that he doesn't share Jane's memories, you will then cancel out your hardest evidence - The fact that Red John allegedly read Jane's memories to kill his happiest one.

3) We know that what drove Jane into the Red John investigation are the death of his mother and daughter. To assume he is Red John is to assume his other personality killed his family to start the chase. You may say that it's exactly what happened, but as far as we know, Jane was mentally stable before the murder.

4) (Connected to 3) Jane's family was killed while he was doing his act of TV. To assume Jane is Red John is to assume he hired someone to kill his family, or he was at two places at once.

5) And the hardest evidence to prove Jane's innocence: His happy memory (Aylin - not sure how it's spelled) was murdered overnight, or afternoon the previous day (Inferred from when the maid found her) Since we are shown footage of Jane sleeping in the office during all previous day and through all the night, he could not have possibly killed her.

So here you go - 5 reasons why Jane isn't Red John.
Note, I didn't name all the reasons. Follow the same logic, and you will find more proof.