For me, nothing. I don't like the 3D touch on my new 6s Plus....seems like a pointless gimmick to me. I also am not a big fan of how fast the touch ID is, so I like the touch ID on the Pro.
I'm going out on this limb and say that next year won't have a new pro. We will be in alternating years for iPads. This year was pro, next is air 3, year after that is pro 2, etc.