Make the showing of the various drupal_set_messages configurable in the settings. If turned on the behavior is the same as current module - if off no drupal_set_messages are displayed. This, combined, with issue http://drupal.org/node/121054 would allow you to totally customize the notification behavior.

A second part of this could be support for a 'message' $op of the hook created in http://drupal.org/node/121054 that would allow the set messages to remain turned on but offer more flexibility in modifying their content.