Multiple Repositories per Project
Using named branches is fine, but it can sometimes cause headaches with multiple heads etc.. It would be great to support storing multiple separate repos per project to allow the most simple and powerful form of hg branching, a local clone, to be stored server-side. This would also be a useful feature to allow large projects to keep the repos small by using several feature repos instead of a single monolithic one.
Since the wiki is already a 2nd repo associated with a project, hopefully it won't be too difficult to implement the addition of N more and the associated GUI and admin features to support it.
In the future it would also be nice if the separate repos had optionally separately configurable ACLs.
Google recently implemented this feature in their hg based project hosting: