I have an extremely crazy idea, which could potentially if it were true, be a massive bomb the writers drops on viewers. Just hear me out. It's not an accusation as much as a "What if...".

I've been very outspoken in my theory that Red John will turn out to be Alex Jane, Patrick's father. Let's look at the timeline...

1980's - Patrick and Alex work together conning people and making decent money.
mid 80's (perhaps 85 or 86 - Patrick runs of with his wife and his father becomes enraged. 
1988 - First Red John Killings, but Red John becomes inactive for 10 years.
1998 until present - Red John kills again (including Patrick Jane's wife and daughter.

A few things before I continue. 
1. We never hear what happens to Patrick's father.
2. In 'Red John's Rules' the family friend tells Patrick Jane that his father was manipulative and exploited people's personal struggles to make money.
3. In "Strawberries and Cream", the man posing as Red John says "I will get a new name, a new face, and make a new life for myself"

So here is my CRAZY idea:
Early 1980's -> Patrick Jane works with his father as con artists in the carnival.
Mid 1980's -> Patrick Jane runs off with his wife and his father becomes enraged over this.
Late 1980's -> Alex Jane creates a small cult following. They from the farm on which the first Red John killings happen. Here Alex kills the first victims. 
After 1988 -> It is mentioned that Red John stops killing after the 1988 killings so. Alex Jane is responsible for the 1988 killings. Over the next 10 years, Alex Jane changes his appearance and his identity completely and becomes ... BRETT STILES. His group 'Visualize' grows and he continues to feed financially off of others' emotional needs. He becomes rich and powerful and has influence in all law enforcement agencies.
1998 until present -> Alex Jane (Now Bret Stiles) avenges his son's running off by murdering his wife and daughter and placing Patrick Jane in a cat and mouse game with himself.

Seriously, this explains absolutely everything. 
1. The handshake : Of course someone would believe that if a man met his father, although it's not his father anymore, he would recognize this man. Alex told Lorelei that he and Patrick worked together, and thus she can't believe Patrick did not recognize Brett Stiles or befriend him.
2. The comment about Alex making money off of others' emotional shortcomings falls in place because visualize does the exact same thing.
3. Brett Stiles says with confidence to Patrick Jane "I KNOW RED JOHN BETTER THAN YOU EVER WILL", and he says he knows Patrick's father. 
4. The Tyger falls into place as well, "Thy fearful symmetry" and the imagery of one man who created both Patrick Jane and HIMSELF, Brett Styles.
5. Patrick's father would have known about Patrick's happy memory from the carnival.
6. Even though Brett Stiles may not seem like he could do this himself, as the episode "Strawberries and Cream" indicates, Red John has many people working for him. Any one of them could be involved in any murder so far.

I know this sounds crazy and Bruno Heller most probably wouldn't pull a 'plastic surgery card' on us, but as I said, WHAT IF it were the case...?