There really needs to be a method of inserting category group names and separators in the list of categories so that a category doesn’t have to be needlessly divided into excessive sub-categories.
We need to be able to create category assignments by query, again use the softwares very capable advance search feature. We at least need to be able to assign a link to a category so that we can use search result urls to accomplish this.
You’ve also got to add a method for mass category moves.
Expand / Collapse all categories in the “Manage categories” section of the Admin control panel.
I’ve told CS-Cart this aswell. 
But it’s good to get more input.