It was designed to update once and run multiple sites from that one install, has anyone tried that out yet ?
I have been running the beta for a while now to test out the multiple site bit, was using WordpressMP before that but it had its own set of problems.
However 3 is very good IMO, themes and addons can be installed on a site by site basis to answer ergophobe's concerns. Still had the eternal permissions problems though. All of my themes installed perfectly on it, however I don't really use many plugins but would assume they won't work until you try them, it seems to be a fair old rewrite under the hood.
I recommend installing it on a test server and having a play..