The one biggest improvement: If you have purchased audiobooks through iBooks, you used to have to purchase them on your Mac and back them up or you wouldn't be able to access them later. If you didn't, you had to call Apple's help desk to have the audiobooks reset.
Now, Apple has changed the Purchased section of iBooks.
Now, not only can you find your purchases, you can find updates to purchased books, but you can now also access (and re-access) your purchased audiobooks.
They do also have a feature that allows your other books to be stored on iCloud for later downloads, however I have a lot of PDF's that I manage via iTunes on my Mac and can remotely synch what I want to my iPad. Because of this, and the storage issue, I've declined that for now.
But the Audiobooks? Yes, Apple can finally say they have scored on this one.