NQ/HQ crafting materials should share the same slot
My retainers are full up and I like having a wide assortment of crafting mats available so I can make stuff to sell when my gil gets low. My reasoning for this is because otherwise whenever I wanted to make an item to sell or use for a lower level job I would need to go out and gather it or buy the materials. I do not consider it an "interesting choice" to have to choose which materials to keep on my retainers and which I have to go get.
With that out of the way let me explain one way they could have them stack. I don't know how they would program it but this is what I would have it be like:
Have every crafting mat stack up to 198 (99HQ/99NQ) and the amount of each could be seen by mousing over the stack.
I think this would be a great way to help alleviate inventory issues.