1) Creating stubs dynamically means you need to run the standard wsdl2java utility to create the stubs and then load the classes using reflection.
But this is not a clean approach. If your consuming application requires those new changes then recompiling and modifying your application is the standard approach.
2) There is Dispatch Client model in JAX-WS programming allows you to create the request messages dynamically from the end points. But the intended use of this feature is different
Take a look at
http://www.ibm.com/developerworks/websphere/library/techarticles/0707_thaker/0707_thaker.html
3) If you are concerned more about the code base maintenance then just create a interface to access the client stubs. That way you can treat and maintain the client stubs as a separate artifact.
Then changing the client stub dependency version will solve the problem.