iOS 9 changes a fundamental concept of syncing – the syncing of apps.
In previous iOS versions, apps that were updated on any iOS device would simply be transferred to the PC during a sync.
However, apps that were updated/purchased on an iOS 9 device will not be synced to the PC. This is due to Apple’s new policy (from iOS 9 onwards) of only loading the appropriate components of an app to a device. For instance, only the iPhone related components of an app will be loaded into an iPhone, the iPad artifacts in the app will not be loaded. Hence, this means that the app on an iOS device is not 100% complete. This is the reason why apps updated on an iOS 9 device will not be transferred to a PC during a sync. A PC will only contain apps that are complete.
Apps that are updated on the PC will be synced to the iOS device.
One way to maintain the identical set of apps on a PC is to manually download the apps that were downloaded on a device to the computer as well via iTunes. An easy way to see in iTunes the apps that are not present on PC, but present on your device is to go to the App Store > ‘Purchased’ (on the right hand side) > ‘Not in my library’ . Strangely, it is not able to sort the apps in chronological order even after sorting by ‘Most Recent’.. Is this a bug or something, I’ve no idea.
The other way is to enable automatic downloads in iTunes.
Edit > Preferences > Store > Automatic Downloads > tick the checkbox for ‘Apps’ .
I’ve to agree that this new policy change is not well communicated to the general public by Apple. Such major changes should be explained clearly. I faced the issue of numerous apps being stuck on ‘waiting..’ after syncing and was wondering why. I did some research and this is what I am able to conclude so far.