Do prefer the menu system, or do you reply on the key words, associated with each article to find what you want? If the latter, are the terms effective in locating what you want or do the queries return a lot extraneous stuff as well? Are there any particular views, you think would help, or see changed?
Originally the site was just using a free tagging vocabulary called category. This allowed users to simply add whatever terms they thought appropriate, to describe their content. To gain some control, a second multiple select vocabulary was added that allowed terms to be related together in a hierarchical way, much like a menu tree. All content required at least one, or more terms be used to describe the content. Terms are preset by an administer, providing a course tuning. Used in conjunction with the free tagging vocabulary allows users to fine tune this.
This does not prevent the selection of terms that don't necessarily relate to one another. Nor does it help if users select to few, or to many terms.
Do you think the dual classification as helped classify your articles, or is it a hindrance?
The taxonomy manager module was added to better manage some of these issues, by allowing terms to be more easily moved between vocabularies; and facilitated a periodic clean up.
Different sections within the site,may mean there is e little overlap between terms. It may be advantageous to define vocabularies, specific to a section,