iCloud and the App Store have been a PITA ever since I got my 6S+. Backups don't install properly, they don't save properly and I still don't have a fully set up phone. It has been over two weeks now.
For instance, my old backup which has worked perfectly on other iPhones caused problems on my new phone. Alert tones were muffled and when I tried a reset all settings the phone crashed & got stuck in a bootloop at the Apple logo. A hard reset didn't sort it and I was left with a DFU restore as being the only option. I installed my old backup again and the same thing happened, muffled alert tones and a bootloop crash when I reset all settings.
I then decided to set up as a new phone and set about the painful process of installing all my apps, photos and videos manually. Not having to do this is one of the major benefits of owning an iPhone so I was pretty peeved. Anyway, a couple of evenings later it was all done. I backed up to iCloud and considered my phone 'back to normal'. Unfortunately I made a grave mistake at this point and deleted my years old backup from iCloud, thinking it was FUBAR.
Then I discovered a couple of minor bugs in iOS9 that others weren't experiencing, so I decided to erase all data & settings and reinstall my new iCloud backup. This would ordinarily have been a completely troublefree experience. Not this time. None of my photos & videos loaded, and a few apps were 'dead' which meant that I had to delete & reinstall them. I erased all data & settings again, then reinstalled my iCloud backup. The exact-same thing happened again, so now I'm left with basically a brand new iPhone experience with zero backup and a couple of evenings work down the drain.
I created this backup from an iPhone 6S+ running iOS9 and yet for some reason it appears to be 'incompatible' with my 6S+ running iOS9. This isn't the experience I expect from Apple!