You must be joking. The finder is the manager of files. No app should ever take over that task. EVER. We are already generating confusion with apps that try to mimic the finder. I have seen more people get all confused about this:"are the songs I see in iTunes files? What happens if I delete them, are they erased?" , total nonsense because it isn't clearly defined to the user that the song you see is a link to a file and not the actual file.
Here's another nonsense: You connect a camera to your Mac, iPhoto automatically launches, creates a new folder, moves the files form the camera to that folder and places the photos in it's library, all this is done behind the scenes, the novice user has no idea the iPhoto just created folders without him knowing. Now, are the pictures he sees the files? How does he know that? And where exactly are the files at?
Anytime you hide info you get into trouble. It's just not a good solution.
Well that is the job of iPhoto and iTunes they are for managing and storing pictures and music. How could they accomplish that task if they did not store and organize these items in the same files.
I wouldn't call the file hidden. Clearly in the tool bar are files called Movies, Music, Pictures. Clearly marked in those files are iPhoto pictures and iTunes music.
I don't see the problem being in the implementation. People just need to know how the system works. When iPhoto imports your pictures it places them in a file called Pictures.
Consistent storage for iPhoto is important because it nondestructively edits pictures. iPhoto needs to know where the original unaltered picture is for this to work.
Doing away with the way Apple currently does this leaves the job to the average user to set up a file, organize thousands of pictures or thousands of songs in that file, then link iPhoto or iTunes to that file.
Of course there is the option in iTunes to store your music whereever you choose.