1. The ability to "merge" files [manually], so that if you have the same song on two or more albums (e.g. the original album, a collection and a compilation) you only need one physical file, and link to that from all places (thus also updating a common playcount etc for the song nomatter which album you're listening to). Having multiple instances of the same object is bad database design...
2. Better and more specialiced conditions e.g. the ability to say (A and B) or (C and D) or (E and F), without making three helping playlists and on random playlists the ability to say (like in Party Shuffle) "play higher rated songs more often".
3. Playlists in folders (like iPhoto).
4. The possibility to split tracks and remove parts (to seperate and identify bonus tracks, without having to have two instances - this problem is not that unlike #1) - or at least that when you set a Start Time or Stop Time in the option for a track that the iPod also gets (and reacts to) that information - its very annoying when I've "cut" away a bit of a track, and it sounds like I want it in iTunes, but NOT on my iPod mini (might be an iPod problem, but I had to get it off my chest )
5. Continious play (for albums like Pink Floyd "The Wall") without making the intire album into one track.
6. That iTunes recognices CD-Rs longer than 74 minutes, so you can burn 80 min CDs.
7. The ability to have an album connected to the main artist, but still mark collabarations with "Artist1 feat. Artist2" or "Artist3 with Artist4" and let them show up when you browse Artist1, -2, -3 or -4, respectivly. Now it will make a new arist (an folder) with "Artist1 feat. Artist2" and if you choose Artist1 and than the album, that track will not show in the browser...
8. Artwork seperated from the music files (in its own metafile?) and just linked in, it takes very much unnecessary space to have the image included into evey songs file (at least with larger scans). Again poor database design...