One feature that WPMU has been lacking for a while is the ability to track site-wide activity in addition to the activity on one of the independent silo blogs.
As a publisher working with WPMU now, I’ve found the ability to have lots of blogs running simultaneously great, but I often wish there was a way to use all that information more easily for a site-wide portal page (similar to how Lyceum, another WP derivative, allowed).
Among the things that this would allow for is tracking site-wide most popular posts and recent comments (instead of just over a single blog).
Just a thought.