The d-pad still doesn't scroll lists (this was explicitly cited as being worked on).
The cursor doesn't start at the top of a list when you open a menu. This is incredibly frustrating with the pause menu. You have to do this bizarre "where's waldo" of where your cursor is and which d-pad direction you have to push to get ti to snap to some random item on the list before you can know whether you need to go up or down to get to the menu item you want.
D-padding over an item should highlight it. This not only saves a click on most interfaces, but alleviates the issue of not being able to read what a gear item does without having to first equip it and then go back into the menu.
These three changes would make it considerably more bearable for us controller users.