The ZS GUI was designed to read version from ZF1 directory, so when ZF2 was released as GA and included,
there was no way to "merge" the two because of separate architectures, hence separate directories, so the ZS GUI will keep showing the latest ZF1 version.
The recommended ZF application deployment is to include the library with the application,
so we only provide the latest version for new projects or as an alternative to using GIT/Composer/Pyrus.
ZF2 can use a ZF2_PATH ENV var so both frameworks can co-exist even if your PHP include path points to ZF1 /library.
Also, .htaccess of each application can set a different ZF path independently.
Hope this helps!
Happy New Year 2013 :)
Zend Support Team