A factory reset would be good, if only so that a user could reset a Library back to defaults to check what is there, and hence diagnose issues.
Storing the machine name with the backup would be good, and if Restoring to a new machine, ask if the Access Key should be used from the backup. Default to No, so users who don't know what it means don't cause network issues for themselves.
On Upgrade, have the installation program find all the old Libraries and ask the user which MC version and Library they want to use for the Upgrade. Default to the Main (Default) Library from the previous version, which what is supposed to happen now. Make this work when there are multiple versions of MC installed on the machine.
Do all you can to ensure that the Windows File Associations come across to the new version of MC. This has been a problem area for me, but I suspect that is because the Upgrade installation doesn't always find the previous Library. I know Windows doesn't let a program assign File Associations to itself, for obvious security reasons, but if more can be done that would be great. Remove associations with previous versions of MC. That will stop old versions being launched when someone double clicks on a file with an old association.
While I'm here, make sure that the Windows Shell Integration is removed for the old version, and added for the new version, or just updated.
In recent upgrades it seems that some settings get forgotten, not because they are not in the backup, but because new features clash with the original settings, so those settings are set to defaults. Providing a list of such settings that get reset would help people through the upgrade process, as they know what to go and check. Possibly this information could be included in the Release Notes along with the change that prompted the issue, because sometimes it seems to happen during updates, rather than upgrades.
Make sure all settings are included in the backup, and in the transfer. Sometimes new settings don't seem to get into the backup initially after they are created.
However... I was looking at the Zone information stored in the Windows Registry in the past, MC seems to keep a record of all Zones ever created. I suspect that this has caused me some DLNA Dynamic Zone issues. It would be good if a backup only stored current Zone information (Zones in the Library now), so that I could completely uninstall MC including all Registry information, and when I reinstalled and Restored a backup, only that Zone information will be present in the Registry. A bonus would be if the Zone numbering was reset as part of that process, although that may cause issues for people using MCWS to interact with specific Zones. I haven't investigated this issue completely, or come to a conclusion on what the underlying issue is, but I have noticed lots of redundant old Zone information in the Registry.