An update on this: if you prefer to have your GNOME Shell to always use a dark/light variant with the same accent color of the main theme, you can now tune this more:
gsettings set org.gnome.shell.ubuntu color-scheme prefer-dark # To always use a dark shell
gsettings set org.gnome.shell.ubuntu color-scheme prefer-light # To always use a light shell
gsettings reset org.gnome.shell.ubuntu color-scheme # To just use the default, in sync with default theme
For example, this is a light theme with a prefer-dark shell:
