Like most people who are presented with a series of checkbox options, I tend to check them all, unless of course there is a cost associated to them. However, when trying to squeeze out every last bit of optimization from a backup or migration you should be aware that the more options included, the more operations and processing that takes places and unfortunately the longer it will take to complete. Therefore, it is important to understand all the available options, what they are designed to do and whether or not they are critical to the success of your project. If they are not, then you may consider leaving a few unchecked (as much as this may pain you to do so).
Here is a small list of a few options that can take a considerable amount of time to complete:
•Design and Master Page customizations (migration)
•Include All Mailboxes or Include All OneDrive for Business sites (backup)
•Include All Versions (migration and backup).
•Item level permissions (migration or backup)
•SharePoint Designer Objects (migration)