Assuming none of the types you process reference these "skipped types", then you could use an external bindings file to specify that they correspond to an existing class so that a new one won't be generated. If these skipped types are referenced then references to this fake class will be brought into your model.
binding.xml
<jxb:bindings
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
version="2.1">
<jxb:bindings schemaLocation="beta.xsd">
<jxb:bindings node="//xs:element[@name='person']/complexType">
<jxb:class ref="com.FakeClass"/>
</jxb:bindings>
</jxb:bindings>
</jxb:bindings>
Full Example