I didn't mind the shuffle. Heck, we've seen it since S3 in Africa (it will never get better than that, though). I don't necessarily think it was designed to favor one tribe over the other. It might easily have turned out similar to All-Stars, where only one (Amber) ended on a different tribe.
I do blame the editing this season for our inability to predict a boot. We've had no real story arcs other than Steph, Gary, Lydia, and to a lesser degree, Bobby Jon, Blake, Margaret. So out of 18 originals, we don't know that much about 2/3 of them. We knew more about Jim in the first hour than we did about Morgan, Brianna, and Brooke after four. Before, the shuffle, where were Brandon and Blake's loyalties? Was Cindy in a tight alliance with any of the men on old Nakum?
I think Judd did the right thing by aligning himself with the former Yaxhas now on Nakum. I think he'll end up going further in the game.