I just texted a friend this same thing.
Since the reincarnation of the original lineup they've been playing a ton of the same songs. What's It Feel Like To Be A Ghost, Error Operator, Decade, Liar, 180, El Paso, Spin (occasionally) and a one or two other tracks are like all they play off the albums that don't include Nolan and Shaun Cooper. Not to say they aren't great great songs and I haven't enjoyed seeing them live butttt I'd liek some variation too.
Songs I'd love to hear this band play again:
The Union, I Am Fred Astaire, Number 5 With A Bullet, Little Devotional, Slowdance on the Inside, My Blue Heaven, Twenty Twenty Surgery, Miami, Sink Into Me, WHere My Mouth Is.
I would guess the main reason they tend to rotate the same WYWTB and Louder Now songs is because Fred did quite a bit of writing for those albums. More on Louder Now, I believe. So, I would guess there is some sort agreement, be it mutual or legal that they will not/cannot play those songs Fred is responsible for writing. With New Again, I am not sure who did all of the writing, but I think it mostly comes down to most fans and the band don't like those songs all that much. Combine all that with the TAYF response from fans, John and Shawn being back, and wanting to play self titled songs too, it gives the sort of rotating setlist they have had the past year or so.