The best way I have found to describe subcategories to those who have worked with AutoCAD before is to liken them to layers. While this is an oversimplification, the idea that you turn on or off a specific subcategory and then you will visually see the result of your selection within the view is an accurate one...mostly.
When I turn on a specific subcategory of a category (for this example, let's use Plumbing Fixtures), the category's view checkbox is automatically turned on as well. This is logical. What isn't logical about this process is that any element (model, annotation, etc.) within the Plumbing Fixtures category that hasn't/can't manually be assigned a subcategory is still "turned on" with the turning on of the Category. This means that annotations and symbols (which cannot be assigned subcategories) are on if you want any subcategory turned on. If you load in a Plumbing Fixture family from an outside source and they haven't properly implemented subcategories (surprise, surprise there), all of the unassigned elements will also show up, whether they're of the selected and desired subcategory or not.
This very much breaks the entire usability of subcategories and forces users to use filters in place of logical subcategory implementation.
Unassigned elements should be on their own "Unassigned" subcategory, at the very least. Annotations and the like should be allowed to be assigned to specific subcategories, but at minimum they should have a default "Annotations" subcategory to be assigned to.
These types of changes would vastly change the usability of subcategories, and therefore of Revit itself. It would make trade coordination within sheets much easier to manage, and it would help users dealing with families built with varying degrees of subcategory discipline.
