I found your post interesting because in a recent project I had to decide whether it would be best to organize some nodes around taxonomy or referenced nodes. This is the classic "everything is a node" dilemma that fields in core for Drupal 7 only made it more dramatic. In this sense, we could also think about RIP the user module. However, I still think some of these assumptions hard-coded on both the taxonomy and the user module are quite useful. Perhaps moving both of these modules to a more entity like approach with these assumptions soft-coded would be a more elegant solution. But until then, long live the taxonomy and the user module! :)