The problem is the wholesale model in general. All of this distorted pricing in both the physical and virtual spaces comes from the fact that retailers have so much control over the pricing, and are in turn sold physical books at a very low price in recognition of the fact that large tomes of paper are heavy and expensive to move.
Digital sales should never have been wholesale in the first place; publishers should control eBook prices, just like developers do app prices. Meanwhile on the physical side, considering that most dead tree sales are through Amazon anyhow, it's probably time to reevaluate the wholesale model and move closer to how video games and movies are sold. The market is going to be a mess so long as you're using two very different pricing mechanisms for the same item, and in the end it's not going to be dead trees that are in the majority of sales.