I saw you were looking for ideas, so here is my contribution:
Be able to select which categories to include/ exclude for autotagging.
Use parent/ children for one to many tag relationships. Search based on children tags (and/ or parent tag) and the parent tag gets assigned to post instead of the children. This is handy for synonyms and topic tagging.
Be able to choose to use only the local tags database.
The ability to choose whether to mine for tags in posts by entire words or parts of words.
Mass edit/ assign tags that come up as a search result in the admin manage posts without having to open posts. (Source: the Better Tags Manager plugin by Keith Dsouza)
Be able to edit tags of single posts in the admin manage posts without opening posts. (Source: the Manageable plugin by Aaron Harp)
Be able to confirm for each post or mass confirm for selection of posts before adding tags automatically to posts?
Be able to choose whether to add tags for published, unpublished and/ or drafts posts?
(In the long term) (for example XML/ CSV) import of subject oriented tag dictionaries. For example engineering, architecture, and biology (open source community project) tag dictionaries.
Don’t get me wrong very impressed with the plugin.