It sounds like the backup story on Windows Phone is set for a massive improvement.
The latest from BUILD 2014 is that Windows Phone 8.1 will now automatically back up the isolated storage of 3rd party apps to OneDrive.
Isolated Storage will be backed up once per day. The data used will not count towards your OneDrive allotment.
The start screen will also be backed up and can be restored across devices, much like on Windows 8.
If users are unhappy about having their app data in the cloud developers can opt out of the service either by specifying it in the app manifest, or storing data in the local cache folder. Enterprise and side loaded apps will not be backed up.
Via Justin Angel