When docking your ship in a port, you should be able to use the (otherwise useless) cranes to load cargo. Clicking any valid location on your ship would have the crane buy a crate and place it on your ship. You could click a few times to queue multiple spots.
The crane could also be used to sell cargo and open sealed chests. You could queue multiple of these in much the same manner.
You could also use the same system to sell Large Cargo. These would be equivalent to 8 crates of cargo, packed onto a pallet that covers the area of just 4. Not only would they be more spacially efficient than standard cargo, but more time efficient, with the caveat being that not all places would sell or buy them.
To balance these additions, you might nerf the profit margins on existing shipping routes. Loading up your ship to the brim would be faster and easier, but if you’re not smart about it, much of that profit would be eaten up by loading fees. This would also go well with the introduction of a market system, where the prices of various goods fluctuate due to events (eg. towns hit by tsunamis will pay more for food, trends cause specific products to be momentarily popular, etc)