Came here to say this. The software itself is really awesome, and they have done some great UI/UX work here, but the hardware experience is still very frustrating. I'm really surprised they haven't iterated on the hardware. It's been what, two years since they started sending out the first set of scanners?
While a case solution on the iPhone would work well, I can see why they might not do this for the iPad (designing an entire case, just for card swiping, for such a large device seems silly and wasteful), but something along the lines of this would be a huge improvement over the current card reader design (basically, it fits around the corner of the device, giving it much more stability): http://olloclip.com