What is stopping iBooks from having everything amazon does? I thought I remembered Amazon strong arming some things with publishers, but I couldn't say anything for certain....
The primary thing is the world's largest publisher (Random House) telling Uncle Steve to get bent when he said "it's the Agency model or you're not selling in iBooks". They basically said "Fine, then we won't sell in iBooks. You don't get to dictate our pricing model."
Ergo, Amazon has titles from Random House, where they pay the wholesale price that Random House sets for the book and then turn around and sell it for whatever they want (which is almost always less than books from Agency-model publishers), while Apple doesn't.
They also have vastly more indie books, because their large marketshare (somewhere in the neighborhood of 82%) makes them a much more attractive marketplace than iBooks.