How to create custom taxonomy URLs without taxonomy name?

Here is some code that should do the trick:

//Creates special permastruct that turns all terms of cities into slugs
add_action( 'init', 'set_rewrite' );

function set_rewrite() {
    //Get terms
    $terms = get_terms( 'cities', array( 'hide_empty' => false ) );
    //return if no terms
    if( count( $terms ) < 1 ) return;
    $slugs = wp_list_pluck( $terms, 'slug' );
    //create term regex
    $termregex = '(' . implode( '|', $slugs) . ')';
    //New query var
    add_rewrite_tag( '%cityname%', $termregex );
    //Add permastruct
    add_permastruct( 'cities_struct', '%cityname%/' );
    //refresh if new term added
    if( get_option( 'update_cities_struct' ) ) {
        global $wp_rewrite;
        $wp_rewrite -> flush_rules();
        update_option( 'update_cities_struct', 0 );
    }
}

//action to refresh rewrite rules when a new term is saved
add_action( 'created_cities', 'refresh_cities' );
add_action( 'edited_cities', 'refresh_cities' );
add_action( 'delete_cities', 'refresh_cities' );


function refresh_cities() {
    update_option( 'update_cities_struct', 1 );
}

//set city name to the taxonomy cities
add_filter( 'parse_query', 'parse_cities_query' );

function parse_cities_query( $query ) {
    if( !empty( $query->query_vars['cityname'] ) ) $query->set( 'cities', $query->query_vars['cityname'] )
}

Basically this creates a special permastruct that uses the slugs of the taxonomy cities as its base. It creates a query variable called cityname, which only accepts the slugs of the taxonomy and then sends the result to the proper taxonomy query variable.

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