Here's a status report on the menu-related issues for 6.x that I'm aware of - please add to/update this list:
RTBC in the queue:
Adding new node link with the same path will hide other links to the same node
http://drupal.org/node/179578
Tabs rendering broken if non-existing item is in path
http://drupal.org/node/179474
arbitrary number of arguments in router path are not supported
http://drupal.org/node/177488
patch code needs review:
Ugly breadcrumbs
http://drupal.org/node/176748
Inconsistent titles and breadcrumbs at various levels in aggregator
http://drupal.org/node/173188
menu.inc should clear page and block caches
http://drupal.org/node/170514
Login menu item - can't be edited
http://drupal.org/node/169018
using slash in profile category hides profile fields
http://drupal.org/node/111481
patch code needs work:
Cleanup menu/arg usage in function node_revisions
http://drupal.org/node/167090
breadcrumbs in D6 include current page
http://drupal.org/node/139303
Open issues - please join in and help:
page title fix: filter module
http://drupal.org/node/175779
Improve menu code to handle callback breadcrumbs
http://drupal.org/node/155624
content types without form listed in node/add
http://drupal.org/node/169049
Improve menu module usability - additional permission
http://drupal.org/node/154471
won't fix:
Let Primary and Secondary links be arbitrary menus (won't fix?)
http://drupal.org/node/160168
Resaving a link double serializes options
http://drupal.org/node/172725
past accomplishments (committed patches):
page title fix: taxonomy module
http://drupal.org/node/174254
performance boost - remove array_shift from menu.inc
http://drupal.org/node/172764
page titles are broken when outside the active menu or on a callback
http://drupal.org/node/172754
Menu system fix- setting the active path
http://drupal.org/node/148677
Moving the "Administer" menu item breaks pages
http://drupal.org/node/159527
split up menu module
http://drupal.org/node/170651
Menu update from D5 -> D6
http://drupal.org/node/147657
menu needs to offer Primary and Secondary links blocks
http://drupal.org/node/171019
Introduce "Tail arguments" wild card in menu paths
http://drupal.org/node/157510
menu and book module UI - only show allowed parents in select
http://drupal.org/node/165675
Let Secondary links be children of Primary as in the Drupal 5 menu system
http://drupal.org/node/160168
Use API function to delete menu links during rebuild
http://drupal.org/node/155621
Optimize menu queries and indices
http://drupal.org/node/154470
The modules admin page is still not coded for the new system
http://drupal.org/node/136386
refactor book_block to improve performance
http://drupal.org/node/164348
Allow custom menus to be deleted
http://drupal.org/node/156626
Node types aren't going away when module disabled
http://drupal.org/node/147061
Improve performance of access checks and add localized sorting
http://drupal.org/node/154469
custom menus - error in submit function
http://drupal.org/node/156770
Menu system UI problems - moving items between menus
http://drupal.org/node/151055
Remove node/%/% from comment_menu
http://drupal.org/node/157773
Menu - Typos and Code style fixes
http://drupal.org/node/156782
Menu - Reset form fix
http://drupal.org/node/156793
Drupal Menu - Fixes that make menu module work in D6
http://drupal.org/node/151583
Clean up hook_help() by providing real Drupal and router paths
http://drupal.org/node/154064
access perms too strong at admin/content
http://drupal.org/cvs?commit=71682
http://drupal.org/node/136585
multiple menu support
http://drupal.org/node/137767
User load and node load need to validate arguments
http://drupal.org/node/148678
Menu - Single Tab Issue
http://drupal.org/node/132226
Menu system: Default tab behavior
http://drupal.org/node/115847
Menu module for D6
http://drupal.org/node/147656
Allow localization of built-in menu items
http://drupal.org/node/128082
Prevent duplicate pages (active URL alias)
http://drupal.org/node/106094
Menu enhancements
http://drupal.org/node/125763
Menu inheritance is wrong
http://drupal.org/node/138703
Menu bugfixes: 40x pages, external items, parenting
http://drupal.org/node/131009
Custom menu items
http://drupal.org/node/130991
Handle negative weight and position properties in menu definitions
http://drupal.org/node/127172
Menu fixes and enhacements
http://drupal.org/node/126128
Fix tab bugs
http://drupal.org/node/118183
Tabs Episode 2: Attack of the Clones
http://drupal.org/node/115748
Reimplement tabs
http://drupal.org/node/113603
Move the menu rebuild after the profile is finalized
http://drupal.org/node/113788
New menu system: faster and less memory
http://drupal.org/node/34755