This is one of the reasons that the Kindle app is still #1 for me. That's the difference between a company that is primarily in the book selling business (at least that's the way Amazon started) and a company that sells electronic hardware (Apple).
One of the things I can do with Amazon that I can't do with iBooks is browse online at amazon.com on my PC (which is much easier to do than searching on the iPad) and then download it to my iPad when I start the Kindle app. iBooks takes place entirely within the iPad universe. You can't even read your iBooks on your computer... not yet anyway.
Even though I have all the eReading apps from all (that I know of) content providers, no one can beat Amazon in terms of selection. Price wise, sometimes other sources beat their price, but Amazon is my "go to" source for eBooks.
Of course, YMMV!