Over a year ago when the Due was going to use the SAM3U I did a design using that chip
Then they changed chips and I lost interest but a small SAM4 board with a decent backplane design and intelligent use of the features would be nice IMO.
Forget the IDE, anyone using such a board will be over that I think. You could use the Due libraries though, most of the peripherals will be the same or pretty close.
These days I'm more into LPCs, but I still occasionally think about resurrecting this design.
Rob