I think for me the Bower API allows a lot of possibilities. Being able to save the type of plugin into the correct folder is perfect. Allows separation of themes, menus, components and extensions.
I really like the idea we discussed around using the adapt package, which in turn allows us to run
$ adapt create theme "cool-theme-name"
and this puts all the necessary files and templates into my themes folder ready for me to start my theme.
Command line is definitely the first requirement and I don't see the UI version until much later.