I have nothing against XDoclet. It eases the development process for many developers. One issue I see is standards/maintenance. If somebody develops some custom doclet tags, be assured that they will not maintain them for ever.
Instead with the introduction of annotations in JDK5, you can get the power of xdoclet in a standard way. Plus EJB3, J2EE 5 as well as JSR-181 annotations for webservices all aim to ease development pain and the wrath of xml files.
I feel annotations are the way to go for developers.