iTunes 11 hasn’t just brought huge changes to the way that apps sync, the backup process has changed as well.
Now it is possible to choose whether to have automatic backups continue to be done with iTunes, or to be synced up with iCloud. Go to the Devices page in the upper right corner, and click on your device. It should open up Summary. Now, you will see the Backups section. This will give you the choice to Automatically Back Up to iCloud or to This computer. Choosing iCloud will make the syncrhonization process in iTunes much quicker.
As well, the manual backup and restoration process has been improved in two ways. One, it is now front and center in the Backups section. Second, it’s now even more convenient, especially for power users. Third, it may actually work now.
The iTunes manual restore is recommended over restoring from an iCloud backup in a pinch for many reasons. The main one being it is faster, as it does not have to redownload apps to a device, it only has to reinstall them from the computer. It will also properly restore apps from multiple iTunes accounts without tripping the restore limit that comes with iCloud restores. If apps are downloaded from multiple iTunes accounts on to a device, then those apps can only be restored so many times in a 90 day time period, even if restoring from a backup made on a different iCloud account. This manual process through iTunes restores them without needing to input a password again.
The manual restore will work with switching devices as well, as all backups made with iTunes are available when choosing to restore. To switch a device all you need to do is connect it, explicitly back it up, then restore to the new device. This may be the easiest way to upgrade from one device to another, or switch from iPod to iPhone, with the convenience of iCloud available if a restore is necessary and a computer is unavailable, or if a device is lost and hasn’t been synced with iTunes recently. It’s very flexible, and a welcome addition to iTunes 11.