Setup of my new 6+ from my 5s backup is missing app data

Check with the application developer. Not all applications store data in an area that is backed up by iTunes and/or iCloud. Also, some sensitive data is not backed up unless you are using an encrypted backup. One example is the Heath application on the iPhone. Your health data is not present in your iTunes backup if you are not using an encrypted backup. This is a privacy protection system. So, find out what the app developer has to say about whether or not the data is in your backup.

The backup is designed to backup settings in case of restore. It is certainly not a mirror image

You should be storing everything on your computer.

About backups in iCloud and iTunes - Apple Support

cphooper wrote:

So the unencrypted backup to my Mac is complete in iTunes speak, because they expect to have data not copied i.e. the health data, but not a mirror image? crud 😟

The manual is pretty clear about what is and is not saved in an unencrypted backup. It's also logical. And the developer of the app can also flag it to not back up if the backup isn't encrypted. As an unencrypted backup can be read with any of dozens of apps or a SQLite database manager, how secure would your data be if anyone who found your phone could just back up the phone to a computer and have access to all of your passwords?