Why would you be considering a larger or faster processor?... And now a Due?. Unless your code is plain vanilla, It will have to be re-written and what of testing? Again?.
A 644 would fill the bill as to larger code space. However you would still be at prototype until the code is checked out in it's final resting place.
Remember that you are writing for a totally different core with an ARM processor. Not our lovable little 8 bit'ers and that's a whole different world.
When I did engineering, not so long ago (5 years). I made a prototype board for code that was written for me. My job was the product design and development. I had an engineer that wrote sample code that was breadboarded first to my spec and it was an iterative process where the first article from the board house was used to wring out my electronics and the code that drove it. The parts were ordered at that time and when the boards were done I had two stuffed, one for me and one for the SW engineer.. Funny thing but it is iterative for both the design and the designer The more I did that process the better I got at designing.
There is also that I had a bargain with my employer.. He stayed in his office and didn't look over my shoulder... and I fixed any mistakes I made. Fortunately we only ran 100 Bd's at a time for the first 100 or 200 boards but it did make me aware of my errors because I did this on my time. YMMV.
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