I think that as far as crops go, there should just be other forms of storage for them. A vegetable crate that can hold variable amounts of vegetables depending no what it is. Hundreds of peas, or 50 cucumbers for example. Could be liftable type and a stationary type, with the liftable one able to interact with the other. Stockpiles are nice, but i'd rather see more variety in our storage options then just piles of food on the ground.
The same could be said about most of the other things we want better storage for. Rather than stockpiles, just implement different storage containers that function in a similar way but require more input then right clicking the floor.