Why do FHS reformers never get anywhere? It's because they only worry about the problems they want to fix, not solutions they're throwing out. Why are UI redesigners met with fear? It's because they're only worried about making the new UI do X, not explaining how it meets or fails to meet existing needs.
This is also why backwards compatibility is so important: It means that the things you don't do right can at least still be done. On that note, why throw away file paths and not just tag each file with its "real" path and in the UI make it appear as if folders and a strict hierarchy still exist? It doesn't make things less semantic and it doesn't break anyone's head.