Thanks for the feedback.
Regarding your idea to use extended properties as a flag to exclude objects from a SQL Compare synch script, I'm not so sure this would be the right place. It's more likely that we'll extend the SQL Compare project concept to allow objects to be more easily excluded from a comparison. Is this something that would work for you too?
Currently you can uncheck certain objects in SQL Compare after the comparison. These selections should be saved with the project, meaning they won't be scripted when the project is run again, although they still appear in the comparison results screen.
Red Gate Software