I have been working with a rather large cluster of categories, containing some complex hierarchies. It has highlighted to me a need for something a little more flexible to help create a menu system and organise categories. Currently one way to build a complete menu system from the taxonomy is to output the entire hierarchy a loop. This is useful but has it's limitations as you cannot easily control the order.
The menu feature of wordpress is a part solution to this problem but when working with large taxonomies it becomes rather cumbersome. The biggest issue being the somewhat arbitrary reorg of a taxonomy in the categories sidebar (which is supposedly a feature but I fail to understand the 'float to top' benefit). This makes adding items to the menu system very problematic because the structure of your taxonomy is abstracted from view in favour of this alternate ordering.
I think it would be a great advantage to be able to drag and re-order the taxonomy in a similar way to the menu system. It would mean you could use a loop to build a list and be confident the order is correct or be able to tweak if necessary, also being able to re-order for other practical reasons would be useful.
Accompanying that adding a device (Checkbox / Select) to make a taxonomy item available to the menu system (with retained hierarchy) would make the management of menus and taxonomies more complete.