Custom taxonomies registration is very easy with Custom Page Templates plugin, which allows you registering them right from WP Admin. Under CPT Settings find menu item "Taxonomies"
Custom taxonomies can be created as regular posts, this is new post type created specially for configuring custom taxonomies. The performance concern has been resolved here, by pre-compiling all custom taxonomy settings, so during custom taxonomies registration on each page load this process is blazing fast. On each such post type change (created new, existing updated or deleted), system automatically updates global taxonomies config.
When you create custom taxonomy, there are different metaboxes which allow you setting all arguments required for custom taxonomy registration.
After you create or change post type, the system will automatically flushes rewrite rules (once) and this custom taxonomy becomes available in WP admin and frontend.