Ok People, here is a list of the Red John episodes:

Season 1: 01, 11, 23
Season 2: 08, 23
Season 3: 03, 09, 16, 23 - 24
Season 4: 01, 02, 07, 11, 13, 17, 23, 24
Season 5: 01, 05, 06, 07, 08, 13, 16, 18, 19, 22
Season 6: 01, 02, 03, 04, 05, 06, 07, 08

People have been complaining that this Red John reveal felt rushed.
If you look at the episode numbers, anyone can see there is a growing frequency in Red John episodes. It's actually nearly perfect placement of Red Johns reveal.

And although Thomas McAllister was not who I thought was going to be Red John, he was only one of two from the list I thought it was, and I knew it was either him or Partridge, because it was always going to be one of the two dead guys.
So I'm not disappointed it's McAllister, because none of the evidence negates it being McAllister.
You at least have to admit that to yourself.

But to me it was a disappointing episode. And not even because, like a lot of people think, Red John turned out to be a bit of a whiny chump begging for his life. But because the way in which he took control of the situation wasn't at all clever. It was just a simple magic trick.
Which you could argue is why it worked. Red John may have been look for some elaborate trap didn't see one, had a false sense of security and that's why he went for it.

However, I much would have preferred a double episode with Jane managing to work out that it was McAllister and catching him.

If Heller had just made Jane somehow force Bertrams hand, catch him and make him believe he was still free, and force Bertram into the position of meeting Jane.

Perhaps if Jane had worked with the CBI, and arranged a scenario where the CBI would get close to Bertram but let him escape a couple of times, really turn up the heat on him and have Jane slip him a phone and Jane tell him, 
"I know you're not Red John, but I know you know who he is. Lets arrange a meeting and you can use my car to escape if you tell me who Red John is". 
Bertram see's a trap and doesn't trust Jane, but he explains that he doesnt care about Bertram, he only cares about Red John. He doesn't want the CBI to catch him, he wants to kill him himself."
Bertram's desperate.
The the Feds come in and do what they do, and Jane does what he does.
Bertram phones Jane a the park and Jane arranges the meet, tricking Bertram like he does into accepting the church as the meeting place.
When they do meet up, Jane covers his bases in case Red John is watching and is determined that Bertram is Red John to his face and the meet was just a ruse. 
Jane claims that the CBI are on their way, knowing that RJ would know they've been disbanded, but Bertram wouldn't. Bertram decides to hurry things along, gets Cordero to pull the gun and so on. 
Bertram gets shot, RJ turns up as McAllister, who feels an extra little nugget of pride of outsmarting Jane again when he hears Jane think RJ is Bertram.
And what happens, happens. Jane has the pidgeon because Cordero only padded him down as far as finding the gun.
Then on the grass, by the pond, when McAllister says 
"Don't you want to know how I knew the list?" Jane says 
"I live, sleep and work in a room surrounded by windows, all you'd need is a telescope. I don't care how you know."
Then with his hand pressing harder on his throat tells him,
"But when you set the concussion bomb in my house, you pulled me, Bertram and Smith to the next room. You placed a decoy body, set of an incendiary bomb and faked your death. That's when I knew it was you." You see confusion on McAllister's face.
"You got Partridge to change your DNA record before you killed him, that's how you fooled forensics. I knew I had you, but I couldn't tell anyone because you'd have run. I had to let you think you outsmarted me again, I had to make you think I thought it was Bertram."
Fear runs across McAllister's face and Jane squeezes more on his throat,
"I knew you'd want him dead. Just like Reed Smith. You always want them dead. And so I used him as my bait. I knew you wouldn't be able to resist coming to see me get it wrong again."
McAllister tries to keep him self alive a few moments longer,
"The list..... I'm psychic...."
Jane puts more pressure on his throat,
"Then you should've seen this coming"
Jane then squeezes the life out of him, as McAllister tries to push Jane off but hasn't the strength and he dies.

If that had happened, I'd have been much happier.

No way in hell Macalister is red john.

No way macalister after janes "breakdown" could offer him a new life. What could the sheriff offer him? He isnt styles or kristina frye and cannot offer him salvation in any way, hes just a guy with power. RED JOHN DOES NOT FEAR DEATH!! He doesn't believe in hell as we know.

Macalister runs tiger tiger what would he offer jane, a tattoo ? He told patrick he can give him a new identity. Reede smith didn't get a new identity when he joined.
Red john wants to turn patrick. He wants him as a "disciple" as jane says . Brett styles is alive . He is red john. Van pelt is his niece or a follower . Jane knows all of this too. Its a long chess match.
Styles told patrick he is dying but we all know styles NEEDS to resurrect like jesus after his death. Macalister pulled styles out of the house before the bomb.
Styles will not appear to the world because he will be arrested for faking his death . He will do it in church with only a few watching to spread the word . Jane will be there . He will get the info from van pelt somehow .

HELLER ONLY RUSHED THE FIRST 8 EPISODES TO GET THEM OVER WITH. IF MACALISTER WAS RED JOHN THEN HELLER WOULD of MADE THAT THE SEASON FINALE!!!

There is no way the private investigator was murdered to keep quiet! SHE WAS LEFt ALIVE ON PURPOSE!!! Why would red john let her live long enough to tell pj about the tattoo? How could she of seen the tattoo!!! If red john was silencing her he would of killed her quick with his knife . Simple as that.

Partridge said "red john has not killed in years" and he's right . Macalister was posing as red john and maybe with the help of partridge too. But the REAL Red john will be revealed soon. Very soon.

I surely do think Red John is dead and done with.

That said, I'm not so sure about Stiles...  Yes, he said he was dying, but perhaps he was getting out of the line of fire so to speak?  If he knew Jane was getting close, and if there was some sort of relationship between Stiles and Red, maybe his dying 'story' would allow him to disappear if Jane found out and defeated Red John...  Maybe Stiles got blowed-up good anyways despite a relationship... 

Tom might have had the DNA records switched with two bodies to save Stiles as well...

Stiles might just be talking the talk when he says he knows more than Pat or John could ever know, but then again, he might be involved--the whole Tyger group... 

I don't know how, but I have a feeling we aren't done with Stiles.  The girl who tried to knife Jane at the end of 'Red John' sounded like she was from Visualize to me.  We also know that Stiles is very manipulative and followed.  That and he definitely has the resources which could have helped a NAPA County sheriff do what he did...  But so did many other members of Tyger I'm sure...

When the FBI rolls in at the end during 'Red John' we see an old man in a suit walking away with white hair...  Waldo?  Stiles?

I think bringing him back would be a smart idea from a writer's perspective--he'd make a good finale.  Stiles would allow the Mentalist to end this season (and possibly series) with some familiarity, yet something new as well.  A link with Visualize could help answer some burning questions we have left over.

So while I think John is gone, Stiles might show himself again...  Perhaps he along with Michael Kirkland...  I don't think that Tom necessarily followed Stiles, but some sort of relationship could clear-up some of our questions...  

But of course, maybe Stiles was just talking the talk.