It's not a kludge - it's how application are meant to be installed (and on mac and Linux too, though the names are different). The application goes in Program Files, and shouldn't include files that need to be changed after installation barring updates, settings go in UsersyouAppDatasome folder, those are the things that the application needs to change but the user isn't intended to access directly, and documents (files that the user will open and work with directly) go in the Documents folder (which by default is also in the Users folder, though it can easily be moved).