Both have similar performances, however even if Apache XMLBeans seems to present better performance, I normally choose JAXB because I don't want to increase the size of my applications with 3rd party tools.
With Apache XMLBeans you need a small package around 2mb, it's probably easy to learn and well documented. Have full support of XSD specification and namespaces, and mapping only via XML Schema Definition (XSD). It also seems to use deprecated API’s.
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