The Due has a more capable chip but many of those additional functions are disabled by Arduino. (Real time clock, Ethernet, watchdog, DMA...)
Do you know why they are disabled? What is "watchdog"?
Some of the additional features useable on the Due are important to some people (CAN bus, dual I2C, 12-bit ADC, DAC...) If you're not sure if you need one of those, then stick with the Mega.
I doubt if I would use the CAN bus.
I suppose that the Mega has one I2C, right? I think that the Mega has a 10-bit ADC, right? I think that the Mega doesn't have a DAC, right?