Exposing and Accessing MBeans are really two completely separate issues. Once you have exposed the MBeans correctly users should be able to access them from a different machine using whatever client suits them. This client should be generally agnostic to your specific server implementation.
Details on how to expose your MBeans for remote access are covered here:
http://docs.oracle.com/javase/tutorial/jmx/remote/jconsole.html
As for which client is the most user friendly, I have generally found JConsole to be very easy to use. Once connected remotely to your application's JMX connector, the user should not have to manage any other special options other than the arguments passed to your MBean methods. If your users need a custom UI, you may want to think about building your own following the docs here:
http://docs.oracle.com/javase/tutorial/jmx/remote/custom.html
You can also look up the Oracle docs for "Monitoring and Management Using JMX Technology".
Edit:
In rereading your question - it would be helpful to know if you are developing both the application that has the exposed MBeans and the application that is consuming them. If you own the MBeans you may be able to help the users by trying to split apart operations that take a lot of parameters. Also consider how you are grouping your operations and whether your naming convention is user-friendly. I think most clients available are going to present you with the same issues if you have a large number of MBeans in one JVM.