With iOS 9 apps don't seem to be copied back, possibly due to a new feature for developers that has/is being rolled out
The App Store and operating system optimize the installation of iOS, tvOS, and watchOS apps by tailoring app delivery to the capabilities of the user’s particular device, with minimal footprint. This optimization, called app thinning, lets you create apps that use the most device features, occupy minimum disk space, and accommodate future updates that can be applied by Apple. Faster downloads and more space for other apps and content provides a better user experience.
An iCloud backup and restore should work (for those apps etc that are still in the store ; tones and audiobooks won't be redownloaded by an iCloud restore).
For an iTunes restore you will need to redownload the apps on your computer's iTunes so that they are in the Apps part of your library, that is where the restore will look to pick them up from