The iCloud folder on a OSX system does exactly that. It contains a folder for each app, but you are also able to save whatever else in your own folders. At the moment that file structure is not visible on an IOS device but I assume this will change with the new iCloud app is IOS 9. At present you are able to create a hierarchy of folders within the iWorks App folders, though this hierarchy is not visible on an IOS device. Hopefully this too will change.