I can't see why pin mapping should be any problem at all. Am I missing something?
I think the SAM has fewer PWM pins (10?) but you're right everything else should map easily, as long as you dumb it down to be similar to a Mega.
That said, if for example you use the external RAM interface (even just for 8-bit access) you lose some ADC inputs, likewise with using PWM pins, there goes more ADCs.
Also, I haven't counted but if you dedicate the SD interface to an SD card (and you would be crazy not to) you will lose 6 IO pins and I think that (along with the XRAM) brings it down to < the 54 a Mega has.
TXD2 and ADC12B0 are both on the same pin and not muxed to any others, I guess that's not any different to A4/5 and I2C on a standard Arduino, you have on or the other but if you want to say put an RS232 transceiver on the TX pin you have a problem.
Anyway, I doubt the Due will have any of the above features and as I said if you just create a simple Mega-look-alike it should work well.
Rob