bperrybap:
I prefer RTS over DTR for autoreset because with RTS you only get an autoreset when
code is being uploaded to the board.
But with DTR you get an autoreset every time the port is opened by an
application which means you can't open the serial port to talk to the arduino without reseting it.
An interesting twist on the brain-deadedness of using DTR rather than RTS is a phenonemon I discovered only recently: On some Windows systems, connecting or disconnecting another device on a different USB port can cause the DTR reset to occur on a USB connected Arduino! Coding Badly suggested this may be due to a background "helper" application that probes the USB ports whenever a system change is reported by the OS, although on my system in question I haven't been able to identify the culprit.
Sheesh. Why did the change from using RTS to DTR occur anyway? Was there actually a rationale, or was it just one of the random "design" decisions passed on without explanation or prior discussion from On High?