I currently have 12 footed chest stacked on the biggest shelves back to back for random materials, 3 separate for food, and then other storage solutions around. I spend an equal amount of time trying to stack already stored items as I do trying to decide if I just need another box or if I need to spend a day pulling everything out to restack them together. If all the storage bins had an option to link together and auto stack together, we could then just deposit into our bases storage without issue. Also being able to Search storage would make it so we could find potions or enchantments without having to try and store them separately.
Palia has an interesting setup where all containers just contribute to the same storage pool and from any container you can see all your storage, filtered by tabs for broad categories.
They have two types of storage, one for general storage and another for protected storage that will not be used in crafting.
However, Palia lets you have storage and build storage only in your small home instance, so it's more structured and less free-form than Nightingale.