I'm not sure if this has already been mentioned, but I know that a number of people have commented on the whole smuggled pigeon not being discovered when Jane was frisked and not believing it to be remotely plausible. I'm going to go out on a limb here and say that it actually wasn't a completely ridiculous outcome. I've watched the leaked episode, and watched the real one again looking out for it, and the pigeon was on the inside of his jacket on the same side of the suit as the gun. In terms of Jane being frisked, Cordero or whatever his name was, was looking for signs of weapons- most probably, knives and guns. And so, when he found the gun in Jane's pocket, he probably noted that it was bulky when he patted him down, but also probably dismissed it as just the gun and not thought to check inside the jacket once he'd found the hard object. It's been done in movies before- the whole gun being kept on the outside of a coat as a prop while another weapon was concealed underneath it, and so it was less likely to be discovered. 

In this case, said weapon was a pigeon, and while it didn't seem to make a noise or anything, Jane possibly had a trick up his sleeve for shutting it up- or it was too busy stuffing its face with breadcrumbs. Or that could be another plot hole. I have to say, if they'd done this episode completely right, as in perhaps had Jane talking it out with Red John about previous clues and how he'd figured it out accompanied by flashbacks, and maybe a bit more confession from Red John about anything, really, I would have thought the pigeon thing was actually a nice quirk, quite fitting with those previously seen in the show. However, problem is that in the absence of any other twists/satisfying explanations, the pigeon thing seems completely ridiculous and out of place, what with it being the main twist and apparently the hero of the episode. One theory summed it up quite nicely: 

http://www.whoisredjohn.com/See-a-theory-Red-John/14016

Anyway, I think the other most disappointing thing was the fact that the show has demonstrated the ability in the past to explain convoluted plots, and the fact that the Red John saga was not really dealt with all that well seemed to indicate that the writers really didn't have much of a plot about the character, and instead of avoiding becoming like "that show with the polar bears" they managed to achieve just that. Especially with the fact that BH came out and said that he would leave the concept of whether RJ was/wasn't a psychic for the audience to decide because he didn't want to offend anyone.

Um, no. You designed this character, you should know everything about him, he either has superhuman powers or he doesn't. If he doesn't, explain how he found the list- it's not one of those little mysteries that in years to come fans will look back affectionately and say, "We never did learn how he figured out the list"- you want to introduce the concept that he's potentially psychic, you either go the whole way on that track of thought, or abandon it altogether by introducing an alternative explanation. 

So, this episode was very disappointing. I liked who they picked for RJ, but hated the fact that there so much potential for something big in that showdown, and instead of using all their time to build tension/explain things, they instead kept ruining the tension and wasting time by cutting away to the we've-seen-it-before-on-every-procedural-crime-show-ever investigation/out to get the team crusade against the key characters by another law enforcement agency. 

I'm glad the episode is only rated 6.4 on Imdb, and hope that the rating continues to fall.