Been reading through this thread and all of the information has been very helpful. Thank you!
That said, I'm having a problem I've not seen anyone write about, which is the apps themselves not updating. iTunes 11 on my desktop Mac is showing 83 apps that have updates. This is the library of apps for multiple devices (iPhone, iPad, etc). All of the apps have been updated on my iPhone and iPad, but are only out of date on my desktop Mac. Of course clicking the "Update All Apps" button in the bottom right-hand corner of the apps library page seems like the obvious solution. The files download, and be monitored via the download pop-up window. However, after each app update has downloaded, iTunes 11 does not recognize the app as updated. Perhaps it is not installing the update properly? Of course I've restarted iTunes many times. I've also tried transferring purchses from my iPhone and iPad (with the updated version of the apps) to no avail. Any ideas? Your input would be much appreciated.
While current version of any mobile app is not really neccesary to have on the desktop, it seems like a master library of apps is a good idea for purposes of syncing multiple devices without the extra steps of managing the updates on each device separately. Of course if it doesn't work, then I don't see the point of iTunes managing apps at all. Perhaps it should just stick to traditional media (music, movies, tv shows, etc).
Hopefully much of this issue will be resovled in iOS7, with the automatic updates features.