All the suspects on the list are boring. It will be ok if it is Partridge, but it is way too obvious. I would really Red John to be Rigsby. That would be totally unexpected and fun to watch.

P.S. Cho would be even more surprising, because no one expects an asian red john.

Just some thoughts now.

Now, as far as the list goes, pigeons is a huge clue. So either Red John loves them, or has a bird phobia.

When Lisbon tracks Partridge and goes to that house, there are some pigeons in that house. They might be the reason Lisbon is still alive, or RJ likes her for some reason.

On the next episode, just after PJ talked with 3 suspects in the office, we see a strange looking woman with rough hands feeding pigeons. Could be RJ, dressed up as one. (Sherlock Holmes, anyone?) Smith, McAllister, Bertram are at the office at that time or one of them is really good at putting all that make up on so fast. Also, when Smith, McAllister and Bertram talk, when PJ leaves, it looks like Smith is talking to Bertram more like a colleague, not a person in charge.

McAllister could be RJ then, but RJ has a fear of heights and sheriff sure does not.

That leaves Partridge, Haffner and Kirkland and Stiles.

Assuming Partridge is dead.( He is a CSI, and has weak physique. He won't have rough hands from this kind of work. Plus, when RJ saved PJ from copycats, he lifted PJ with chair easily. Partridge would struggle with this I think. Plus, he seems younger than any other suspect, which makes it hard to see him in charge. Moreover, if he indeed faked his death, why do we see his blade soaked in blood, and then PJ says that Partridges blood was on Lisbon's face? Did he cut himself then? ). Although, there are some clues that he is RJ. His voice is the strangest of them all for sure. Partridge - connection to Blake poetry. Working with surgical tools, and so on.

Haffner being RJ is very likely. He is a good whistler. Is afraid of bugs?. Pigeons eat bugs, Haffner loves pigeons?

Kirkland. Well he is dead. Don't see a point in faking his death that way.

Stiles. It actually makes sense if he is RJ. All other suspects are working for him as a Tyger Tyger thing. He uses them to distract and spy on Patrick, Old enough to be in charge. Visualise is money and power. It just would be a very dull RJ, without much surprise.

So it might be Stiles or Haffner as I see it.
Anyway, I choose Rigsby, because his transformation would be wonderful to watch.("Unusual suspects" style).