With alpha11 I've created a zone--footer.tpl.php for theming zone footer.
Now, with 2.0 version, zone.tpl.php take priority over zone--footer.tpl.php
I would quote part of theme() description:
There are two special variables that these preprocess and process functions can set: 'theme_hook_suggestion' and 'theme_hook_suggestions'. These will be merged together to form a list of 'suggested' alternate theme hooks to use, in reverse order of priority.
I don't know if this is the right way, but I would add a proposed patch