The real benefit of Java on RISC OS isn't the existence of any particular application, but rather the fact that the applications are platform independent. Obviouslly Flash shares this benefit too, the difference being that there are far fewer serious desktop applications written in Flash (but perhaps I'm wrong about this?).
If I want to run an application to perform a particular task that doesn't exist on RISC OS, I'd have thought my best chance would be to find an open source C/C++ or Java application. The C/C++ version might do the job, but will likely involve a tricky porting process, so Java would be a potentially useful source of applications, even if its use *is* dwinding on the desktop.
Perhaps I'm misrepresenting the number of serious desktop Flash applications there are out there, but it's not clear to me that Flash is really a substitute for this type of thing (and that's not to say that Flash doesn't have its own strengths in other areas).
Obviously, none of this changes the issue of speed or remoteness of any likely java implementation.