Personally, and this is just a WAG on my part, is that they rushed the iBooks app into the market. Obviously Amazon is the major player in the eBook (or whatever you want to call it) market with their Kindle device and Kindle app and Apple wanted their piece of the pie. But until they set up iBooks to where you can buy and read content in some other place than the app itself, it will never catch up to Amazon.
Apple may be good at what they do, but they aren't good at everything! What you are seeing is the difference between a company who's primary focus is selling books (at least that's how Amazon started) and a company who's focus is on selling computer products.
