I might have missed where this was discussed, but I don’t quite see how the CP directory solves the problem the WP repo has with versioning.
As far as I can tell, the only version the WP API will serve is the one marked as Stable Tag, although the previous versions are available for manual download. What this does is give the users a false sense of being up to date. For WP releases, the update nag is there, but it can be ignored for years. When it is, all the plugin updates are also ignored because the version numbers don’t match.
I’ve heard that CP will keep 1.x working “forever”, so when 2.x and 3.x are out, wouldn’t they need a different set of plugins? And are they all in one directory? Is the latest version of the plugin the only one that is available?
Take a look at Statistics | WordPress.org to see that there are so many versions being run that the repo doesn’t help at least a quarter of them.