We use JAXB on my current project and I can say that XMLBeans offers much that we desire:
1. Namespace/package/inner class support. JAXB forces you to put all of your XSDs in one directory and all of the resulting Java code is in one package. JAXB also makes no use of inner classes so if you have element buried down in a schema called 'item' you now have a plain top level class called Item. In our medium sized project, our generated code directory has 352 .java files. JAXB is simply unmanagable in a large project.
2. Near 100% XML Schema support. Many nice little tricks in an XSD don't translate to Java code in JAXB.
Disclaimer: I haven't used XMLBeans. I'm sure it has it's warts too.