Some questions and other things.

In my mind, if the BA is still around (which it is), wouldn't they want to hunt down PJ? He did however tell the world about them and he killed RJ (I doubt sheriff is RJ).

How did RJ stay so strong for that long? How did he figure out about everything about PJ (ie. The memory, list,etc.)

Was LaRoche part of the BA? We know he had a big secret (the tongue), so he could possibly be part of it.
Other things:

Patrick makes up a FAKE LIST of agents part of the BA. Emphasis on the FAKJE LIST. This could mean he's made fake lists before -hint hint-

Where can the show really go on from here? You wouldn't end the main story mid season for no reason, something is going to happen, and it might happen next episode (Rigsby and Van Pelt are said to reveal something shocking next episode. Possibly RJ killing someone? Hightower or even LaRoche?)

My guess is that next episode is going to be BIG, and the hunt for RJ will continue. I also believe the Jisbon story line will continue, but I'm not really a fan of it anways