Thanks Graynomad for your reply. 
I did not mention any speed and distance requirements, as these shouldn't be an issue : µCs will be very close (few centimeters) and few data will be exchanged, so few kb/s will be enough.
Regarding CAN, I also read about it (and just read more) : it seems perfect for my usage, but requires additional hardware : 1 CAN controller + 1 CAN transciever per node (but these seem to be quite affordable).
The Due could actually be the main controller of my project, however, it seems that although CAN is present, there is no (official, at least) Arduino API to use it.
I initially planned to go for AVR µC exclusively, but I'm still open to other options that would help me.