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I think a common use case would be to give mobile/iphone browsers a different menu selection than the primary links. This is possible with some page.tpl.php work, but would be handy as an option in the config:
(I created a menu that is referenced by the system as menu-mobile and altered the page.tpl.php thusly:
// foreach($primary_links as $link_name => $link) {
$mobilemenu = menu_navigation_links('menu-mobile');
foreach($mobilemenu as $link_name => $link) {