Some nice improvements here. It appears, though, that Projects suffer from the same problem we've had with Issues: they are limited to one repo. I know there are some tools to manage Issues across repos, but for the most part, the tools seem to assume you work on only one repo, or that milestones only affect a single repo. I would love to see projects/milestones become more capable when dealing with cross-repo issues…
Works pretty well, if a little awkward at first.