One of the things that Apple design paradigms pride themselves on is the Principle of Least Astonishment - designs that match users' experience and expectations, as well as their mental models.

If you use USB to plug your iPad into your computer, click the radio button that says "This Computer - A full backup of your iPad will be stored on this computer" and then clicked on the "back up now" button, what do you suppose would be getting backed up?

If you guessed "Most stuff, with some exceptions for security such as password caches, and oh by the way, certainly not the literally hundreds of PDFs that you have copied manually into iBooks as you ran across them", congratulate yourself - you've won today's prize.

Yep, it's true, your "not-purchased-from-iTunes" PDF collection doesn't get backed up, which is why after I did a software update, my whole PDF collection has vanished, never to be seen again.

Apple, can you even cloud?