Single biggest flaw, as far as I'm concerned, is the inability to script the folder hierarchy. If I want All albums folders to be prepended by the release year I should be able to do that.

Edit: Also, sometimes I have correctly named mp3's, but I haven't tagged them. Itunes gracefully renames my files to 'unknown' removing any trace to the correct name. And, if the files were in a folder prepended with the album year iTunes will kindly create a new folder to hold the files to leave the album art in the original folder. (okay, that last one is Windows only)