I think the main issue here is more than media files: it's the data stored for each app on the device. Music might be a common app with lots of data (and is, as you said, relatively easy), but what if you've saved a 200MB file locally with the Dropbox app? Stuff like that needs to be backed up too, the and the backup service has no way to know if an app's data is "essential" (the user made this!) or just "downloadable content" -- and, all apps would need be updated to know how to re-download after a restore.

It's a complicated problem: it's more than just storing a few hashed and re-downloading from iTunes.