Directories that users and creatives need access to most (plugins, themes) are two- and three-levels-removed from WP's root folder.
Additionally, WP directories currently mix system and user content, making it more difficult to upgrade than it should be.
The solution is User Folders. User folders live in WP's root directory, starting with User Plug-Ins and User Themes.
When a plug-in or theme exists in both folders, the item in User Folders takes precedence. That will allow WP to ship with plug-ins, but still allow users to upgrade the plug-in or use a preferred version without touching system folders.
The old locations (wp-content/plugins and wp-content/themes) shall continue to exist as system folders. The recommendation is that users move all of their plug-ins and themes into User Folders, and it may be useful to enforce this by 3.0.
Paths to User Folders shall not be configurable.