I just upgraded to a new 5s, I have had every generation of iPhone and have been using the iCloud since it started however I have never come across this problem. After I restored my last backup I have all my settings and 50% of my apps are there. However the other 50% refuse to download and don't apear in my list of available apps, even though a couple of them were only purchased recently. I also have no photos or videos, just lots of grey placeholder boxes.
Finnally my music app just crashes as do several options in settings.
I have tried to wipe and restore from 3 seperate backups all with varying degress of success none of them result in a working phone!