selfonlypath:
On some other recent threads, it is clearly observed that the Serial USB link wether HW or SW (low level or high level) have serious speed issue. One way to perceive this, there are many other methods and practical tests, is by observing the same *.INO project loaded on mega takes almost no time to USB download but HUGE time to download on DUE.
Comparing upload times for the same sketch isn't particularly a good method to compare transfer rates.
It might be that the same sketch generates much larger code on the DUE than on the Mega.
To be fair when comparing upload times,
you need to look at the sizes of the .hex files and adjust the times
based on the ratios of their sizes.
i.e. if the DUE takes twice as long to upload but the .hex is twice is large,
then the upload speed is actually the same.
--- bill