The filesystem is strictly hierarchal. How do you have one song in multiple playlists without duplicating the songs? How do you propose to make that usable for the average person. History kind of proves that Apple took the right approach in the iPod era. The simple drag files to an attached device MP3 players failed to become successful.
You miss the point with this question. A media player managing playlists certainly can. Or it can manage m3u files. Or it can put them in an sqlite db. Or ...
You posed as an intractable problem unless we adopt iTunes thinking.
