Mostly implemented already: Update a published document using the exiting pickle files (i.e. faster republishing). Still needs some testing.
Being able to specify a freshenv setting before compiling; to allow a full compile of the document.
Rejecting comments is still to be handled, coupled with a web-based tool to send a reason along with the rejection email to the comment submitter.
Ability for reader to add notes to the document and resume adding/editing the notes when returning.
Allow for 3rd party search tools to be used instead of the built-in simple search: e.g. http://haystacksearch.org, or Whoosh.
Add support for other distributed revision control systems (currently only Mercurial is supported). DVCS wrappers for SVN, Bazaar and Git.
Real-time preview of comments while the user is typing (via AJAX). E.g. see the mathoverflow.net site.
Comment administration interface where the comment admin can approve/reject accumulated comments in one go.
Add a Sphinx extension to enable a directive that generates Beamer slides inline in the RST.
Add inline comments as an option (e.g. see Mercurial book website).