1) Possibly merge the iTunes store and the App Store. Or at least rename the iTunes store. Also rename the iTunes app. It's not just about "tunes" (aka music) anymore, and it hasn't been for a long, long time. It's a central store for purchasing all types of media and apps. I might recommend iStore or iMarket. I'm not exactly sure what I'd rename the iTunes desktop app.
2) Rename the Apple ID to iStore ID or iMarket ID. Make it clear that this is an ID, specific to store purchases, which can be shared among family members.
3) Make it clear that the iCloud ID is specific to *you*. Maybe even force users to create an @me.com ID, rather than letting them use whatever ID they want to. Make it clear that this ID is for a single person, but can be used across all of that person's multiple Apple devices (e.g., use the same iCloud ID for Sally's iPhone and iPad, but not for Jimmy's iPhone).
In addition to the confusing aspects which the above could solve, I've also run into some syncing issues with iTunes on my laptop, where it hangs on the last syncing step (I forget what it says). I can wait forever and it won't ever finish, so I end up yanking the cord.