Your question is something I see very often, I would say typical for large bodies of XSD.
Unfortunately, I am not aware of a JAXB-way to control the generation process, not the way you want.
An alternate solution I've developed for this, hence my bias from this point forward, relies on automatic XML Schema Refactoring (XSR). It basically takes in your XSD, and from a set of XSD objects (in your case probably a couple of global elements and maybe some types), it'll generate a subset of XSDs that would only contain the necessary items, no fluff. Having those XSDs put through JAXB, it'll give you exactly what you want. This involves QTAssistant, and its XSR functionality. The highlevel steps are:
- build a new XSR file;
- refer to your source XSDs in an XML Schema Collection
- create a "release": a graphical editor helps you with it. Basically, you match the top level XSD objects you want, and the new XSD file locations.
- Generate the new XSDs.
- Use the new XSDs with your artifacts.
QTAssistant supports command line integration with Maven through the Exec Maven Plugin, but only on Windows.