I would start by looking critically at the Leaflabs Maple for ideas on what an Uno sized board should be (and maybe the Chipkit Uno32 as well), and at the Maple Mini and Teensy 3.0 for ideas of what a nano sized board might incorporate. For a nano, I'd think one, maybe two mini usb ports, and that's it -- and the rest of whatever IO is broken out is on breadboard pins.
I've programmed the Maple, and I quite like them, I think they are quite an elegant design in many ways. (Of course, it's in it's third major release revision by now, so there's been time to get a few things sorted out.) The one gripe I have is the limited capacity of the board power supply -- you have to manage the board power very carefully if you want to power any external devices as well. Certainly more finicky than something like an Uno to work with, but they work very well and are very reliable once you get them setup properly.
Obviously, a nano sized board using the same chip as the Due would make no sense economically, even if it were physically possible to fit. If a peripheral isn't broken out on a dev board, it might as well not be there. And the smaller the dev board, the more limited the number of pins for breakouts. So why would you pay for an expensive chip if a cheaper variant will effectively give you the same functionality?
So I think the idea of a Due mini/nano is somewhat wrong-headed to start with. An arm-based mini/nano perhaps, but a different beast entirely to the Due.