You can try to re-register the default WordPress shortcode:
/**
* Re-Register the default shortcode
* WPSE: 120057
*/
function wpse_120057()
{
add_shortcode( 'video', 'wp_video_shortcode' );
}
add_action( 'plugins_loaded', 'wpse_120057' );
Here is the file in the Shortcodes Ultimate plugin that contains the shortcode registration.