Does wholesale/retail even mean anything in E-books? I know it does, in that Amazon pays a certain amount to the publisher (wholesale), and charges a certain amount to the customer (retail). But, other than that, there is no cost of inventory sitting on the shelves gathering dust when too much was ordered, or loss of sales opportunity because Amazon or Apple didn't order enough. There is just an ePub file which gets distributed over the Internet and some numbers in a database for how many copies were sold to which customer accounts.
Also, you can buy a physical book from anyone. You can only buy E-books from a supplier that is compatible with your E-book reader. I buy E-books from Amazon because I can read them on my iPad, but I could still switch to an Amazon Kindle when their eInk gets better. Actually, I prefer the Sony E-Reader, but I don't want to be tied to their platform.
The DoJ lawsuit is just getting at the wrong problem. Apple taking a 30% cut of its sales is reasonable, and publishers setting the price to sell through its store is reasonable. It is an issue that they are requiring that a book not have a lower electronic price elsewhere, though that is a long-established practice in music and video games, so it is a stretch to argue that it is illegal.
The real problem is DRM and the resulting lack of device portability. A secondary problem is Apple's requirement that any App that runs on its platform either process all sales through Apple (with its 30% cut) or process all sales entirely outside of the App. That is long established practice in the video game industry, so I really doubt is illegal, but it still heavily distorts the market.
Maybe some good will come of the lawsuit, even if the basis for it is questionable, if it results in a change to DRM portability or forcing Apple to relax in-App purchasing restrictions. Hopefully, if Apple loses we won't just go back to an Amazon monopoly. Perhaps alternate platforms are now well enough established that an Amazon monopoly is no longer possible. Or, if Apple does lose and Amazon does go back to its obviously predatory pricing, hopefully the DoJ goes after them with equal voracity.