I just managed to deploy my first Windows IoT Core (Background Application IoT) and Windows Universal (Blank App) via VS 2015 on RasPI2. After a quick scan I wonder if there is any mouse handling (MouseMove ...) integrated in the new .Net framework as well?
From what google was able to tell me, the answer is yes. You're app cannot be headless (so have UI and a screen, which makes sense). Here is the example I was able to find. It seems like movement is constrained to a Xaml UI object.
https://msdn.microsoft.com/en-us/library/windows/apps/windows.ui.xaml.uielement.pointerpressed