Nice to see that you started using Prism 4. First of all, take into account that the product team is using Moq to create its mock objects. That said, there is no guidance about how to mock the Application.Current in Prism out-of-the-box. I assume that you
are trying to test the following method:
protected override void InitializeShell()
Application.Current.RootVisual = (Shell)this.Shell;
Application.Current.MainWindow = (Shell)this.Shell;
In the Prism Library the base.InitializedShell method has already been tested. That said, I am not sure whether the override method in your Bootstrapper should be tested or not, as it contains reference to static classes. A possible solution
for testing this could be create a CodeUI test.
Regarding to test the registration of views in regions, it is something tested in the PrismLibrary, so this might be solved by creating a mock of the IRegionManager/IRegion. You can check similar tests on the StockTraderRI.
Hope this helps.