IDE 1.6 hampers serial speed on Due (SAM3X8E)

_From @cjbaar on November 7, 2016 17:8_

I have been using several Arduino Due boards under the beta IDE (1.5.8). Previously, I was able to successfully maintain a continuous serial connection between two boards (using native Serial ports) at 5,000,000bps. Using the exact same boards and code, but being programmed using a current IDE (1.6.11), I am not able to get above roughly 500,000. This is only 10% of the previous speed. I am not sure what may have changed in the Serial libraries from beta, but I would like request it be reverted to allow higher speeds.

_Copied from original issue: arduino/Arduino#5577_

Start by reproducing the report with Arduino Due boards using the native Serial ports, the reported code, and IDE 1.6.11, comparing roughly 500,000bps with the earlier 5,000,000bps behavior. Trace the Serial-library changes between the beta IDE and 1.6.11; done means identifying the regression and restoring the higher sustained speed or documenting the confirmed limitation.

Written by the indexing model from the issue text.