Add the ability to 'pin' items in your inventory, or maybe set a certain number of slots that don't transfer when you hit the 'all' transfer button. When I want to dump my loot out quickly, if I hit 'all' I need to then pick out the items that I want to keep in my inventory pretty much permenantly. Like the tools I can't fit on my hotbar so I need to hold on to them to swap them out.
Now that we have Pepys Box "cloud" inventory, I want to store my exploring supplies in Pepys and then pin the three ingredients to make a Pepys Box in my inventory so I can access the supplies anytime and anywhere. Same with my extra tools and such.