SharePoint 2010 removes Site Directory template, and you can't create it anymore (almost), but for the compatibility reasons the migrated sites will show the Site Directory.
That comes us to idea that Site Directory template still exists in SharePoint, but it is hidden. Ben Curry provided nice description of how to return Site Directory template back to SharePoint 2010.
The solution is to dig webtempsps.xml to unhide features and then activate the "PublishingLayout" feature via
stsadm.exe -o activatefeature -id 5F3B0127-2F1D-4cfd-8DD2-85AD1FB00BFC
And then you are able to create Site Directory.
stsadm.exe -o createweb -url http://sitedirectory -sitetemplate spssites#0 -title "Site Directory"