my content (nodes) are original to my site, but the terms that describe it (taxonomy terms) are concepts that are part of universal, cultural and scientific truths that exist independently of the content on my site. For these concepts, I only need a name to represent those concepts. Taxonomy.module is a place where relationships of meaning are played out against the content of my site.
Taxonomy.module is basically three unique things:
1. An inflexible hierarchical relationship.
2. Free-tagging or the automatic creation of entities by name.
3. A UI for managing controlled vocabularies and their hierarchies.
The data and UI of taxonomy.module's hierarchical relationship has not kept up with the rest of Drupal.