This improvement is similar to https://redgate.uservoice.com/forums/147879-sql-data-compare/suggestions/4157645-exclude-special-schema-from-datacompare, but I would like to sketch the idea out a little further.

SQL Data Compare should provide a filtering option that allows the user to exclude entire schemas from comparison, or to exclude tables explicitly. This can be done somewhat at the schema level by unmapping an Owner.

But this doesn't provide the feedback on the main screen that I would like to see. There should be an additional Type on the main screen named "Deselected for comparison". Tables or schemas that are not mapped shouldn't be put into the "could not be compared" category. They may be able to be compared, but the user has explicitly selected not to.