I am thinking why would we need the complexity of allowing branches. The union FS should (to my knowledge which is admittedly very less) only have the changes to the underlying fs and nothing else. We should have user level tools that should modify the u-fs to work with a new kind of underlying system if the need arises. The need should arise only during upgrades, and then the distribution should provide it.
I would think that ... would be the ideal name for the special directory containing changes in each directory.