Here is what I came up with so far:
Added edit button at the category headers drectly at the addon manager list, which shows a context menu then once clicked
1) Change assigned addons directly at the category header at the addon manager list
Using LibScrollableMenu with search header so you can search for addon names and the submenus only show those addon names then.
Important: Remove the search term (1) BEFORE you click the "Apply changes" (2) button or ONLY the currently filtered (shown) addons will be kept in the category (all others removed) -> But I think the apply changes button is hidden too if you do not search for "assign" or "change" so you cannot click it until you reset to show all
Here is how it looks if you filter/search something (press button (1) to reset the search):
2) Edit the catgory name directly at the category header at the addon manager list. A dialog opens where you enter the new name and addon list refreshes afterwards
3) Changed the settings menu to show an orderList widget for the categories where you can drag&drop them, use buttons to move them up and down and add new categories via a "+" button or delete a category via a "-" button
4) Assigning addons to categories is still working in the settings menu too but currently there is no easier way to handle it. I'm still trying to add LibScrollableMenu there so you can use the search header in the dropdown boxes
That way I moved many of the handling of categories and addons in categories directly to the addon manager list,
you got a search functionality and I'll add more features like "Add new category" and "Jump to category" via a small "v" dropdown menu at top right too:
Currently testing all, compatibility with Perfect Pixel and Addon Selector addons especially, and will release it as a patch for the original addon then nónce finished.