One thing I would love to see from this is development rules about what can go in each directory. If we get, say, a UI directory, I would like to see something like: no database queries are allowed in UI-directory files; no use of $wgOut (outside of API or development/debugging stuff) is allowed in non-UI-directory files. We could have little RULES files in each directory, and mercilessly revert changes that break them. Likewise, parser/ should have no interaction with $wgUser, for instance.
While we're at it, there's no good reason for skins/ or languages/ to be so separated from all the rest. Either skins/ and languages/ should be moved into includes/, or the contents of includes/ should be subdivided and moved out into the installation root. Moving skins/ would probably break custom skins, though, I suppose.