Hello i did manage to pair rpi3 and the integraded bluetooth with a genuine sixaxis ps3 controller.
if anyone is intrested i did
sudo apt-get install bluetooth
and then
sudo apt-get install pi-bluetooth
idk if both of those is needed but thats how i did. then use retropie config to pair ps3 controller
hope anyone has some help from this.
/mallorz
EDIT: 99% of the times i rebooted, controller was not pairing. had to plug in the usb cable for a couple of secounds then it pairs.
if anyone has a solution for this problem im happy to hear 