I don't know if these are iTunes-issues but:
- Ability for iTunes Servers (ie from a NAS) to be able to stream video content, not just audio
- Have my tv shows show up in order by episode on my iPhone remote
- Allow for multiple computers on a home network to access one iTunes folder simultaneously and edit simultaneously (ie add songs, edit tags) while keeping them in-sync (or *nsync, if you will)
Two of those are fairly specific and likely don't appeal to a lot of people, but I bet the TV episode sorting might.