Linking vocabularies to specific content types (page, story, project etc) is great, and what I think is one of the best features of drupal. However, there are definitely elements of this implementation that could be improved.
I'm curious how much work/how feasible it would be to extend Drupal to have a more flexible based group permissions system. I understand that you can setup "user roles" and assign a user a role, then define that roles permissions.
We are currently working on a redesign of Drupal's administration pages; the goal is to improve usability for both novice and experienced Drupal users.