I have ubuntu studio 11.10 installed with the ubuntu desktop on top of that. using compizconfig settings manager I was able to make the top panel transparent. however, whenever I open Nautilus the top panel goes opaque again. perhaps there is two panels fighting each other.
Unity is a work in progress. especially with 11.10. They focused a lot of development on it, added many new features and squashed a lot of bugs with Unity 5.0
Have you considered upgrading to Ubuntu 12.04 LTS?
I have had no luck with 12.04 and installing the latest version of ubuntu tweak I saw no option to adjust transparency.
so, classicly I reinstalled everything, ubuntu studio with the ubuntu desktop over it. I have a transparent top panel and can adjust the launcher as well. It took a while to find the right combination, but the final touch was using the gnome tweak tool to turn off the file manager from controlling the desktop. Now the desktop freezes and theres no remedy that I know.
1. appmenu qt/ gtk/ gtk3 - installed
2. indicator appmenu - not installed
3. controlling transparency with compizconfig settings manager