I see many complaining about the pigeon thing.

I think that Bruno meant to let Patrick use this "cheap" trick because after all these years of trying all these well thought out plans and traps he failed to get Red John with, he went "back to basics" and just outsmarted him with a small cheap trick.  

How would you have liked this to happen though?I also wanted a showdown but if you think about it they can't have a gunfight, or a sword fight or argue each other to death.  Endless dialogue would have made it stale.  The trick Patrick use was right up his alley and he knew it's something RJ wouldn't expect.

I only feel that the execution of the trick was a bit rushed from a writing point of view. We don't truly see where the pigeon comes from and the way it starts is truly unrealistic: 
Patrick: "Can I show you something?"
RJ: "Sure" *Walks over and holds out his hand . . . uhm DUH!

The rest of the RJ reveal sequence I really don't mind. It was poetic and it was a fitting end. 

The writers have from the beginning of this series had poetry as a huge theme and in my opinion this episode ran like poetry.

There was this monster created by years of hype and mental torture, but he comes to Patrick in the form of a man. A mere man, weak and afraid of death.

I think also that in a continuation of the Bible-themed season we've had so far, it may have been the overall idea of the writers to show the "lucifer" of the series Red John be defeated by good, Patrick Jane and then beg for forgiveness.  Patrick passed judgement on Red John. He says to Red John that he is an evil man. 

Revelations, if I am not mistaken, speaks of a dove that brings peace. Maybe that is where the pigeon comes in. And the church and all of the symbols we have been given in this season.

I think you get my idea.

In short, I think that the reason the episode played out the way it did was because of a central theme the writers followed with the Red John story. He was a "beast" that deceived men and fooled nations to follow him. But he came in the form of a man, who when finally brought to judgement, sought forgiveness and mercy.

Many would have loved a creepy character be revealed as Red John and the episode be an amazing showdown. I also would have loved that.

But the ending that we were given is a satisfying one when you look at how well that theme was carried forward.

If you look at the poetry, the symbolism and take a step back to see the bigger picture, the Red John story was a brilliant masterpiece and the end was the Revelations of this story.

William Blake's poetry and art dealt mainly with religion and Heaven and Hell, and God and the devil.

The next episode is also appropriately titled "My Blue heaven".

Take all of that in and you will come to the realization that Bruno Heller wrote and created a masterpiece of a story.