Just a small update. I was able to get a small spike solution working with WAS 6.0 integrated to a remote WebSphere MQ 5.3 installation. I did have to do all the work in Rational Application Developer, but I did get it to finally work. Actually doing the integration with WMQ seemed to be very much easier than the default messaging baked into WAS 6.0. I really hope that IBM improves this thing (WAS) so development and deployment are easier. RAD is a barrier to entry to using WAS for learning J2EE or working with J2EE as a independent developer. A litmus test should be: Can I build a small application just using a text editor and Ant? If I can't reasonably do this with a little bit of documentation, then the software and the process is too complex.
BTW, this article was very helpful in my integration quest. Bobby Woolf does a nice job clearing away the fog surrounding the WAS platform. I strongly suggest reading anything that Bobby writes if you're working on WAS.