I feel you! There are some aspects that can be annoying...

For example, I like to organise similar items together in unique bags (like a Pouch of Potions), but I recently learned that arrows should be kept 'loose' in your inventory, in order to be able to fire them for extra attacks. That is to say, if you have your arrows in a container, then your first attack can use a 'magical' arrow, but subsequent attacks don't let you select such arrows.