About !include, here what we could improve:
Allow PlantUML to search for files from directory declared in the classpath (and not only in the current directory)
Create a plantuml.include.path Java property that could also be used to declare directories for searching files.
I don't know how to retrieve project's defined include path in Eclipse...
About your second question, what about allowing a hide unlinked command to will hide classes that are not linked to other classes in a diagram. I think it will be usefull for your purpose.