Two thoughts that I had recently that might be applied to future releases:
1) The ability to set multiple hotkeys so that, for example, mousebuttonX1 opens up the lowest level of CD, while mousebuttonX2 goes directly into one of the dock folders. This might have been brought up before.
2) Keyboard control: Call it up with a hotkey, highlights show which icon is selected, arrow keys (or maybe asdf, or some other new scheme) to move the selection, spacebar or enter to select an icon or dock folder, escape to hide the dock if you didn't choose anything. I feel like this could be as awesome as using it just with your mouse. I guess this would require some different method of deciding the location of appearance (center of the main screen or a user decided location), but other than that I feel like it would be another highly intuitive way for CD to be used. This would also open the application up to those people who love controlling everything from just their keyboards.