I do like the more modern look to Supernova, but having the tool bar above the menu bar, separated from the content it associates to is very disjointed visually and awkward for using.
Also, under Linux where I have multiple virtual desktops and can normally right click any window's top bar to selection actions like moving it to another monitor and/or different virtual desktops, or make it available on all virtual desktops - this ability has been removed. No matter where I right click on the menu bar or tool bar, I get only Thunderbird-specific options, no access to either my OS or Window Manager's options for the window.
