Yeah, I'm going to have to echo what Gregory Pierce has been saying in another thread.. The Windows platform is a huge market relative to all X11 systems combined. The accelerated transforms will be effectively unnoticed and certainly nothing that programmers could rely on if the majority of Java installations don't have it.
If you can't please everyone you should at least please as many as you can
.. OpenGL acceleration on Windows and Linux at the same time would be ideal.. but if you have to use one as a stepping stone to the other, maybe it does make sense to start with Windows? (too late for that of course.. but if the WGL stuff can happen at the same time or very soon after X all the better)