WPF 3D is a retained mode API that largely uses declarative XAML to describe the scene. This is very useful for some scenarios, but other scenarios have different requirements.
Silverlight 3D is an immediate mode API which gives full control over the graphics device and the rendering of primitives (triangles). This means full performance and control because there is no retained system or high-level API in between the application and the device. This gives developers the ability to create their own high-level retained APIs, scene managers, and visualization engines on top.