If you are open to changing the wsdl, and possibly the java items involved (complex return object or helper class/interface) that you use, you can change the wsdl accordingly (to the order of the xml items you prefer), and use wsdl2java to generate the interface.
I am following bottom up approach for developing and deploying my web service using AXIS. I first hava POJO that needs to be exposed as web service and then I did java2wsdl and then I have created the server-config.wsdd and deployed the service and generated finally the wsdl. If I change wsdl then it is not going effect the way I send the *response* soap message and chaging the wsdl will effect the client and the way he sends his *request* soap message since client side stubs will determine the request soap message which are generated from wsdl.