I would like to see another kind of dependency graph. It should be more like a map where dependencies flow from top to bottom or right to left. The difference is, that you can drill down from assemblies, to namespaces, to classes, to methods. All of this within one view.

For example: First I see a dependency graph containing all namespaces. When I click on namespace A, it shows me that this has dependencies to namespace B and C. Now I unwrap namespace B and see all classes and all dependencies from A to the classes, instead of the single dependency to namespace B. Then I unwrap class X and see all dependencies from A to specific Methods of class X.

Now we come to the planning. When I have a map of my architecture, I can move elements between containers. For example a class from one namespace or assembly to another. When I am satisfied with my new structure, I press a button and NDepend rearranges the code as I planned.