If the vanilla SAM3XE chip like you can order it from Farnell works with own-built boards, I might develop a smaller version of the Due. I developed a variant (actually: a shield) for the 8bit Arduino for use in industrial environments (think ruggedcircuits but better 
), but boards with the dimensions of the Due or the Mega don't fit in our DIN-rail enclosures.
Perhaps it is possible to minimize the dimensions to something in the range of a Uno by omitting some pinheaders. Then you would have the same number of input/outputs of a regular Arduino, but with the processing power of the Due.