Why can't I restore apps to iPhone 5 from 4s? I recently upgraded from an iPhone 4s to iPhone 5. How do I transfer all my apps to the new iPhone 5? I have tried two times without success:

First attempt:


From iTunes, make "a full backup" of the 4s on "this computer."
From iTunes, restore the backup to the iPhone 5


This transferred all my contacts, call history, messages, and photos but all my 3rd party apps were missing. (Also messages I had received on the iPhone 5 before restoring were over-written... any way to prevent this?) The size of the resulting backup files was only 10GB; about the amount of photos and videos on my 4s. Note: I can view the list of my purchased 3rd party apps from the app store and download/install them one at a time. When I re-install the apps, they retain all their old data and even old icon locations.

Second attempt:


From iTunes, click 'Automatically sync new apps'
Again, make "a full backup" of the 4s on "this computer," (this time using the "Encrypt iPhone backup" in hopes my passwords would also be retained.)
Again, restore the backup to the iPhone 5


This time, the backup size was about 20GB. However, still no 3rd party apps were transferred except a few apps I had re-installed since the last restore.

When I view my apps on the 4s from iTunes (version 11.0.1.12) I see one significant difference from most on-line instructions. Although 99 apps are visible on the right, I am unable to select any of them because they are not listed on the left:



If it makes any differnce, my iPhones 4s still has iOS version 5.1.1 while the iPhone 5 has iOS version 6.

Also, at the end of the restore, the iPhone 5 seems to reboot automatically. However, after waiting for a long time, nothing happened so I restarted the phone manually.

So how do I make a truly full backup of my iPhone 4s and fully restore it on my iPhone 5?
I had the same issue (I use iTunes on Windows 7). I Bought a new iPhone 5 and used the Backup / Restore method to move my stuff from the old iPhone 4S to the new one. The process only restored all the Apple apps, plus Contacts, Phone Calls, and Messages. When I tried to backup again - hoping it would restore the rest - it went through a restore process in iTunes (for about 5 minutes) and then I got the message that my iPhone will restart but never did (I had to restart it manually).

What I also noticed was that, when I retried, the Backup seemed to be very quick.

I called Apple Support who said that there is a problem with the Backup process. I would be able to restore my Apps via the Purchased Apps process but I would lose all my user data (such as games progress). I was extremely frustrated because I use my iPhone and iPad as tools, not game devices.

I went to the App Store on the iPhone and started downloading some of the Purchased apps from the what seemed to be the iCloud. To my surprise, all app data was there (eg. WhatsApp chats, and The Vault data). I am not sure how this works because I never deliberatelly setup app backup on the cloud, but I suspect that the "Documents and Data" == "On" setting on Settings --> iCloud does exactly that, and in return does not include this information on the PC backup.

All seems fine now (at least for the apps for which I care and tried). The issue I still have is this uncertainty on what exactly is my iPhone doing and where is my stuff at any point in time.