I had have an issue too with connecting wirelessly to a PS3 Controller. The hci was always down.

Try adding these 2 lines before the line “exit 0” to the file etc/rc.local

hciconfig hci0 up
hciconfig hci0 piscan

Fixed it for me!

I also forgot to add that I needed to perform the same action that was needed on 2.5.0.
After pairing and restart it seems that sixad is started before bluetooth is up or bluetooth doesn’t come up at all.
You need to do following in this order:
sudo hciconfig hci0 up
sudo /etc/init.d/sixad restart

and then press the PS button on your controller and it should connect.

You can automate it by doing following:
sudo nano /etc/udev/rules.d/10-local.rules

and add following line:
ACTION==”add”, KERNEL==”hci0″, RUN+=”/usr/sbin/hciconfig hci0 up”

save and reboot.

it seems I renamed the original to ps3controller_orig.sh and modified ps3controller.sh.
this is the contents of my ps3controller.sh

rp_module_id="ps3controller"
rp_module_desc="Install PS3 controller driver-mod"
rp_module_menus="3+"
rp_module_flags="nobin"

function depends_ps3controller() {
    getDepends bluez-utils bluez-compat bluez-hcidump checkinstall libusb-dev libbluetooth-dev joystick
}

function sources_ps3controller() {
    wget -nv http://www.pabr.org/sixlinux/sixpair.c -O "$md_build/sixpair.c"
    wget -O- -q http://sourceforge.net/projects/qtsixa/files/QtSixA%201.5.1/QtSixA-1.5.1-src.tar.gz | tar -xvz --strip-components=1
}

function build_ps3controller() {
    gcc -o sixpair sixpair.c -lusb
    cd sixad
    make clean
    make CXX="g++-4.6" CXXFLAGS="-O2"
}

function install_ps3controller() {
    cd sixad
    checkinstall -y --fstrans=no
    update-rc.d sixad defaults

    md_ret_files=(
        'sixpair'
    )
}

function configure_ps3controller() {
    printMsgs "dialog" "Please make sure that your Bluetooth dongle is connected to the Raspberry Pi and press ENTER."
    if ! hciconfig | grep -q "BR/EDR"; then
        printMsgs "dialog" "Cannot find the Bluetooth dongle. Please try to (re-)connect it and try again."
        break
    fi

    printMsgs "dialog" "Please connect your PS3 controller via USB-CABLE and press ENTER."
    if $md_inst/sixpair | grep -q "Setting master"; then
        printMsgs "dialog" "Cannot find the PS3 controller via USB-connection. Please try to (re-)connect it and try again."
        break
    fi

    printMsgs "dialog" "The driver and configuration tools for connecting PS3 controllers have been installed. Please visit https://github.com/retropie/RetroPie-Setup/wiki/Setting-up-a-PS3-controller for further information."
}

also there seems to be a difference in users:

-rw-r--r-- 1 root root 1.7K Mar  1 15:06 ps3controller.sh
-rw-r--r-- 1 pi   pi   1.9K Mar  1 15:03 ps3controller_orig.sh

it is still working fine for me even after quite some reboots :)

Im having the same issue as umut, getting annoyed with the ps3 pad now :(