SirNickity:
I'm really glad someone brought this up. I hate doing things and not understanding why. Thanks everyone for the thorough explanations.My view is that the USB to serial AVR chip code should be tweaked to use RTS rather than DTR.
Six-pin FTDI cables don't have RTS pins. Just DTR (and CTS).
Ummm.... Go have a another look at the FTDI 6 pin connector pinout.
Here is a link to the data sheet. See pages 17 and 19.
DTR is not on the 6 pin cable. It uses RTS instead.
Even the label on the Arduino Pro board labeled it correctly as RTS with respect to a standard 6 pin
FTDI cable.
http://arduino.cc/it/Main/ArduinoBoardPro
But all this is irrelevant with respect to the code inside the 8u/16u AVR chip that has replaced the FTDI chip
for the USB to serial conversion.
To switch to using RTS instead of DTR is a simple code change inside the 8u/16u AVR chip to use the RTS status bit in the messages
vs the DTR bit when driving the output that goes to the other AVR reset pin.
--- bill