I've pushed only a fix that solves an issue when big chunks of data (>64 bytes) are transferred from the board to the PC over USB:https://github.com/arduino/Arduino/commit/95cadfef12c64b37db75acf34411d971d8c36ac5
now I'm looking at the other posts you quoted (thank you) but its hard because they are full of "noise", and its very difficult to get to the point.
The sketch upload is 10x slower because the sketch are 10x bigger, and the speed is the same for all boards (115200 bps).
Blink on Mega2560: Binary sketch size: 1.662 bytes
(of a 258.048 byte maximum) - 0% used
Blink on Due: Binary sketch size: 9.920 bytes
(of a 524.288 byte maximum) - 1% used