Maybe part of the problem is the covered hoppers dedicated to only hauling grain. It's obvious that hopper cars are the most efficient way to haul grain, but the old way of using boxcars with temporary modifications allowed them to be used to haul other commodities the rest of the year. The cost of handling the grain would be higher but there is better usage of your available fleet. Once again, it's obvious the bean counters have figured out that covered hoppers are the way to go but when there are miles of boxcars sitting in storage and piles of grain that need to get out of the weather before it rots maybe looking into how it was done in the old days might be worth while.
Of course the next problem would be which shippers get the efficient, cost saving hoppers and who gets stuck with the boxcars.