The point is that when you use Firmata you degrade an Arduino Uno to the status of a dumb peripheral. You throw away all the intelligence and all of the hard real time reaction you can get from an Arduino. Having said that it does have its place, an arduino, a laptop and Firmata gives you the sort of system offered by the Raspberry Pi, only with analogue inputs and more than one PWM output.
However, now you have produced a beautiful beautiful machine capable of running like the wind and some one wants to reduce it to the same level as a crippled Arduino Uno. I can not see any advantage in running Firmata on a Due in fact I see it more as a crime. It won't run any faster as it is governed by the speed of the serial port.
Would you take a Ferrari and deliver milk in it?
Would you take a thoroughbred stallion and use it to give donkey rides on a beach?
Sorry but I am passionate on this one. 