...funny this post should come up about my old thread.
I actually have come to the descision to use the SAM3X8E - it's readily available, dosen't cost the earth and is compatible with the Arduino IDE which allows me to prove the hardware quickly, then move on to writing my actual code in Atmel Studio.
I'm sticking with the 3X8E for now, and may move elsewhere in the future when I've weened myself off the Arduino IDE completely....
...although, I am looking at the SAM3A4C at the moment for a project - USB Host and Device, SD card support & CAN still - also, much cheaper - £3.88 in 25 QTY from Mouser, vs £5.81 for the 3X8E...