I was fighting with this on a new Ada fruit Huzzah ESP8266 board. I installed their USB driver, or thought i had, since its a Kext I needed to do the restart option-r csrutil -disable thing and then reinstall it.
For a while now I had also had some issues with my Arduino Mega only being recognized on one of my two physical USB ports and just been too lazy to investigate since it was easier just to plug in to the 'back' port not the 'front'.
As part of fussing with the Huzzah driver I noticed and UNINSTALLED (aka deleted) an OLD FTDI USB Kext I must have put in before upgrading to El Capitan.
That seemed to simultaneously fix both my front USB port with the Arduino Mega and allow the Huzzah to work on either port! and here I thought driver/extension incompatibility issues were dead

now... to do carve out some time to actually make something before someone upgrades something!
posting in the hope that my random experience helps someone else struggling with this issue.