I love this idea so I did some mockups:
Desktop
Dash
Window Theme
Indicator Menu
I recommend downloading the attachments and viewing them fullscreen to get a real idea.
The window theme and the indicator menu are not transparent, but I don't think they need to be either. In this particular case transparency adds graphical requirement without achieving a great deal IMHO. I think that an opaque theme which dynamically matches the background colour would work just as well.
Thoughts?