I can't speak to the Pro 3D Ultra, but the prior Pro 3D model differs (from the Comp 3) primarily as follows:
Carbon-fiber-reinforced heel cup/outsole (Pro 3D only)
Molded plastic eyelets (vs webbing on Comp)
Mesh upper material (cosmetic differences)
Toe box construction (Pro 3D is stouter)
Dual-density (Comp 3) vs triple-density (Pro 3D) midsole
In actual use, the Pro 3D seems to provide more stability and long-term cushioning. The Comp 3 is initially cushier, but it seems to break down more quickly. Both models could use more durable cushioning in the heel, moreso than in the mid-foot as it seems the Pro 3D Ultra is now offering.
In general I've found the Comps to be fine for recreational running and dayhiking, while the Pro 3D is the more capable of the two for extended backpacking.
YMMV. It'll be interesting to hear a report on the 3D Ultra.