Hi all,
I finally got around to play with the on-board Bluetooth of the Raspberry Pi 3 and found a way to get it to work with Kali:
EDIT 20/03/2017: I've created a new kernel package that does the entire setup automatically. No need for the steps I've posted before.
Head over to the Re4son-Kernel site for instruction --> https://www.whitedome.com.au/re4son/re4son-kernel.
Happy hacking,
Re4son