Once again Arduino has taken a nice chip and cut off it's legs while mounting it on an compatible platform. It looks like almost half of the Due CPU's available IO pins are NOT accessible on the board (unless you are good at soldering fine wire to .4mm spaced pins by hand). They did the same thing on the Arduino Mega with the atmega1280 and atmega2560 parts (leaving out at least 16 of the IO pins, including the XCK signals so you CAN'T use the usarts in SPI mode!).
If you want to go ARM, you might consider the Teensy3.0 which DOES make all of the I/O pins available (though you will have to solder some wires to pads on the bottom of the board, but at least the pads are there!). The Teensy 3.0 is also about $15 cheaper than the Due.