As I just mentioned this is the first board with the SAM3X we're going to release so there is plenty of opportunities to create different layouts (as a matter of fact we have a new layout we've been playing with for a while)
I think there is a lot of people who prefer to re-use as much as possible of what they currently have before they have to throw everything away.. Our current Eth and Wifi shields, to mention two, work with the Due as they are able to detect and adapt to the whatever voltage the main board is operating at.
Making the board 5v tolerant would have made the it way too expensive. The market is now full of heavily subsidised (even sold at loss...) products that make it quite difficult to fight these battles.
The beauty of open source is that in a few days time you will be able to download the Arduino Due eagle file, design a much better layout and sell your own boards benefiting from our lack of vision 
@Graynomad
we introduced the R3 layout a long time ago and we explained why the IOREF pin is there... some people understood and implemented the correct measures to make their shields compatible, some others didn't ... you'll see a lot more shields made available with the full implementation of R3
m