epinc:
We will only be manufacturing about 3,000 boards a year so I was thinking about even jumping up to the new Arm Cortex based chip they are using for the Due, but it might not be possible due to other hardware engineering concerns (I'm a software guy)
Personally I wouldn't change processors (to a completely different type), unless you want to do a lot more work and testing. As others have said other chips in the same line (like the 644 or 128) would give you more RAM and program memory, and still run virtually identical sketches.