Ok. there's 3 paths here.

1. the route path  .. the router array is indexed via this

  $items['node/%/%'] = array(

    'title' => t('View'),

    'page callback' => 'node_page_view',

    'page arguments' => array(1, 2),

    'access callback' => '_comment_view_access',

    'access arguments' => array(1, 2),

    'type' => MENU_CALLBACK,

  );

2. the target path of the menu item. IE: the EXACT PAGE, the menu item is pointing to.

An example of this would be node/123.. When linking to node/123 using the menu item, 

you would need to resolve the target path from node/123 to the route path 'node/%/%', to be able

to find out what the access permissions are. If this were the link hook, i would be referring to

the 'href' element. (unless you pass the $routes to the menu hook and make it an explicit argument)

3. the menu path. ie: where in the menu this item is located. 

I think this is how i feel the menu data structure needs to be indexed, to be able to say where things are.

Either that or we don't index the menu items at all , making them incredibly difficult to manipulate. (ie: no menu_alter

hook where you could modify individual links). 

Also, keep in mind, that in all likelihood, we will need to have the menu item only inherit from the route. It should probably

also be possible to override the access check for specific instances of that link.