The above features are likely to be refactored into Cocoon blocks (components) thus allowing mix and match cocoon / lenya capabilities. Collectively, this could be labelled the Apache CMF.
The Lenya Repository - does it exist or doesn't it?
Some preliminary JCR work was done in 2006 but it stalled. The only real repository available is Lenya's home-grown filesystem-based one, with separate folders for authoring and live sites file copies for versioning an xml file is used to represent the version meta-data
there's mention of WebDAV and Slide, but they are both just experimental.
v3.0 roadmap talks of JSR-170 and WebDAV building blocks
In summary, Lenya's architecture is gradually improving, but there is no aspect of Lenya that Alfredo doesn't already do much better, and there are so few active Lenya contributors that there should be little expectation of major improvements in the future.