just thoughts, resulting from things that keep me busy all the time:
GUI enhancements:
- SHORTCUTS:
user definable shortcuts. possible options: to bind multiple commands to one key via cycling and reverse-cycling (via some option-key). also, multi-keys (pressing two keys at the same time). this would be essntially the same as being able to define custom option-keys.

apart from all internal commands also scripts sould be made accessable via shortcuts.
the next step would be user definable menus, where a key pops up a menu (much like the "specials", currently accessed by pressing "W").
- CHOOSING TARGETS (for constraints, object-data):
a point-and-click method for choosing constraint control objects would greatly improve useability. instead of typing in the name of the desired objects, the user would press a key labeled "Pick item..". then he can select the object he needs just as always. ESC or pressing the "Pick item.." buttons again would cancel this pick-mode.

for choosing actions for action constraints the user could be offered a similar view as the data-browse window, but where only a hierarchy of armatures and it's actions are shown.
EDIT*:
*deleted* (selection mode issue, already built-in)
EDIT**:
- OUTLINER:
the outline view should be scrollable horizontally, too. right now i have to enlarge the view to see deeper hierarchies.
tell me what you think