The idea is to have the 'repository' and 'ebuild' format decoupled.
EAPIs would specify the ebuild environment, atom syntax etc. which are identified by the EAPI spec. Most importantly, ebuilds should not try to do assumptions about the particular repository structure -- they are just given the necessary files by Package Manager.
Aside to that, there would be a repository format version, reusing metadata/layout.conf. The repository format could also mention how to read EAPI from ebuilds & for profiles/metadata.
Getting explicit repository version would finally allow us to do some cleanup, like moving repository-specific information from profiles/ directory to metadata/. We could possibly also move repository name to layout.conf.
The feature users seem to want from this is to enable "partial" or "on demand" repositories to replace all those nasty hacks people use with rsync excludes.
See radhermit's RFC here: https://archives.gentoo.org/gentoo-dev/message/bb5153a187801924bd520253e206f272.