Usability issues - Access control

This issue seems to be part of the focus of the file repository work being done. I am curious on a more abstract level about where certain files could be accessed and used within Moodle. For example, one of the issues that plagued the quiz module was where the images were stored. Understanding how and in what contexts files are stored might be helpful by looking at each activity (module). What recommendations could we provide developers so that ultimately it seems easier for teachers to make use of the files in a variety of contexts? As noted, controlling access to these items can become complicated but I believe a lot of that has been worked out already in the description of the work to be done on File Repository API. I would be interested if you foresee any usability issues coming out of implementing the file repository api. Are there places that are not using files that could?