I think that Rob Eamon is on the money when he said that it depends on the comfort level of the developer with respect to the amount of flow objects that are used.
My comments address B2B only.
My experience has been that many companies retrain their existing people to use webMethods (that’s how I started) and people naturally gravitate to what they know and are comfortable with. This seems to generate a lot of java coding. I’m not a java coder to begin with, so I rely heavily on FLOW to provide what I need. If I can’t get flow to do what I want (write files for example), then I extend features with Java.
I have seen shops that have heavily leveraged java and when developers cycle through, the java is scrapped in favor of built-in services. I have worked on one deployment recently like this.
I am a proponent of using built-in (i.e., supported) functionality as well because if issues arise, webMethods is quicker to find a solution (I have found at least.)