The problems with the page where one manages the category tree have been discussed numerous times. For example: http://moodle.org/mod/forum/discuss.php?d=78366
I have an improved version of that page implemented in Moodle 1.5. I just looked at the 1.9 code and it appears that the code remains quite the same aside from role-related matters and few other minor changes. This means that it is possible to migrate the changes to newer Moodles.
The crux of changes is:
1. There is no popup menu next to each category with almost the entire category tree.
2. The popup is replaced by a checkbox.
3. Under the list are a few buttons and popups supporting bulk actions on categories that have checkmarks ticked
The bulk actions:
a) moving categories into other categories (as subcategories)
b) moving categories next to existing categories (as sibbling categories)
c) cloning existing categories placing them into other categories (as subcategories)
d) cloning existing categories placing them inext to existing categories (as sibbling categories)
e) toggling category visibility
The big improvement is that there are only a few popups with category trees and they are all the same, that is created once and just reused. This interface can be, of course, expanded with new bulk actions. For example, sorting subcategories was also planned but never implemented. For example, it may be possible to replace the "create new category" button with a category popup to insert it directly somewhere in the tree.
A screen snapshot is attached.