It's not just a miles-per-gallon game. When you're comparing the eco-friendliness of two vehicles, you also need to think through the amount and type of raw materials necessary to produce the vehicle, and the vehicle's respective weight effect on road maintenance.
You also need to take into account the origin of manufacturing and how far the vehicle needs to travel to reach its destination and the environmental costs of that. The Prius is made in Japan, whereas the Soul is made in South Korea - a slight distance edge to the Prius.
Miles-per-gallon is just the simplest comparison. And all else being slightly equal, the mpg environmental cost-of-driving analysis helps the Prius reign victorious.