A small factor Due is in the list of boards that will come out.
Good to hear.
There are a number of issues to solve ... for example with such a big processors it becomes hard to make something that would fit into a breadboard without removing access to most of the pins.
Removing access to pins is generally a bad idea; if a smaller chip doesn't provide a feature, fair enough, but if the chip does provide it and it is not broke out then this is frustrating, because SMD pins are so tiny so wiring directly to the pins is hard.
On the other hand, it may be worth examining whether breadboardability is a primary requirement for a small form factor. Breadboards with their parallel rows of connections impose a constraint on the PCB that is not needed or helpful. If a 'Nano Due' could be connected via multiple
rows of solder holes (or pins, or sockets) around the periphery the more pins could be broken out.
For example: Is it important to have the two separate USB connections or just the "native" connection would suffice?
Since that is one of the defining features of the original Due then I would say yes, its important to keep on a Mini/Nano Due. For example, people might prototype and develop on an original Due, then use a mini/nano Due to mount permanently in the completed project.
There is also the possibility (and this is not without risk, but should be considered) to break away from the 2.54mm/0.1" grid spacing for sockets, and to make a range of small boards with smaller pitch (1mm?) sockets and corresponding small-pitch shields.