Form factor, weight, harddrive technology/speed, controller, and very possibly CPU (whether for lower price or better compatibility. Especially since they mentioned "6TFlops" and faster memory a million times but never said anything about CPU other than 8-core).
GPU and memory bandwidth are confirmed to be faster/more-powerful, but given that it's releasing a year or more after PS4P and that the focus is on being more capable, they better be at the very least.
Personally, the only reason I might get a Scorpio is if there is enough multiplatform console only games that I care about that look significantly better on Scorpio compared to a PS4 Pro. Ah, but then I would have to deal with those terrible LB/RB buttons on the XB1 controller.