Please forgive me if these have been addressed.
1) The ability to know which users/ip addresses have downloaded a file
2) along with #1, the ability to limit the number of downloads per day per user/ip.
3) the ability to scan uploads for viruses. A regular AV can be setup to scan the folders where repository items exist, but it also will scan when files are accessed for downloads, leading to major CPU usage. This could be expanded into a way to "post process" files. For example, instead of a AV scan one might want to allow WAV files to uploaded, then processed into MP3 and saved that way. A good plug-in model will go very far here and even allow #1 and #2 to be developed by someone else (I would do #1 and #2 almost immediately - give me the interface you need and I'll donate the code)
4) The ability to movea repository object from one module id to another....
5) along with #4 a portal wide category list by default.
#4 and #5 would not be an issue except that the Repository gets very unweildy with a large number of files. Mine has thousands of files and I get complaints all the time about paging through so many pages and the paging often gets screwy. Permalinks sometimes don't display the correct file etc.