Hi Dave,
thanks for the post. The GUI for the brainzapr is certainly a good step, especially as it allows you to see the changing binaural frequencies. It is alot of work though, so dont expect it to be available soon. I'm working on it!
As for your other points, I havn't found the volume affecting the system volume settings, and no one else has reported this either. What OS are you using?
The brainzapr does do isochronics, but I dont have many isochronic presets yet. There is a tutorial on how to create your own preset here :
http://www.brainzapr.com/content/view/38/9/. If anyone else creates some new presets, perhaps you could share them with me.
Thanks for the feedback,
Ed