Jon reads backstage sometimes, he made that clear in an online chat, and I think they might be changing it because so many people starting complaining on the boards that the setlists are starting to get boring or all the same, and some were getting shorter. I don't think he picks which towns are more special, I think he's been reading.
He might decide the lists by the crowd. I know in Las Vegas he ended the show early and I have a feeling it was because half the people in section B on the floor were all sitting down.
In Denver someone held a sign asking him to play a song and he all the sudden said something like "Were going to play _____ since she held up that sign asking"
Who knows what's going on, I'm happy, I just wish they could have played One Wild Night and Always at the shows I've been. But theres always MSG both nights!