omeka-cli cannot install themes for now, but you can definitely use it in a small script to install Omeka and a bunch of plugins quickly.
omeka-cli install --db-name omeka [--other-db-options...] /var/www/Omeka
for plugin in Plugin1 Plugin2 Plugin3; do
omeka-cli plugin-download -G $plugin && omeka-cli plugin-install $plugin
Note that you will need the latest (unreleased) version of omeka-cli for this code to work (that means you must clone the repository using git).