I've found that I am able to program an Arduino / Genuino UNO R 3 through Bluetooth in El Capitan, using a Bluefruit EZ-Link. The Arduino IDE does see the Bluetooth link once you have paired it from your computer. That isn't a great workaround for the general problem because it requires adding Bluetooth to every project.
It seems that every USB serial port device is broken in El Capitan. I have a Pololu Zumo 32U4 robot based on a ATmega32U4 which uses LUFA USB (http://www.fourwalledcubicle.com/LUFA.php) and its port is now invisible too.