From my opinion it would be nice to add border for bonds and atoms. This suggestion comes from some other crystal structure programs. For example it can give possibilities to draw white on white (using black border with different thickness) and represent picture in black-white scheme (sometimes it's very useful for presentation in article). It's also helpful to show one bond (or atom) over another (see attached figure). I think there are some more applications for the option.
Thank you for your work!