The missing piece is perhaps some sort of AppImage installer which can be registered as the handler for the AppImage filetype. When ran it could read metadata (packaged as part of the AppImage?) and generate the support files. Ideally would also maintain a database of changes to be rolled back on uninstall and provide a PackageKit or AppStream provider to manage updates with your DE's store.
Now none of that addresses dependency duplication, but thats clearly not in scope for AppImage.