Seems like this is really for people who have more than one DS4, I got it working fine with Mass Effect works well with it. It's weird though I seem to have to reconnect it every time I shutdown and restart my system which is a pain, but I did already bend the end of one my micro USB cables sticking out of the DS4 so I rather do it this way, just hope Sony at least updates it so it connects auto every time like the Bluetooth Blu-ray remote once you register it.
Edit: I did some testing if power on my PS3 with an already registered DS4 pressing the PS button with that controller for some reason it doesn't reconnect after the start screen so have to register it again, but if I start the PS3 with just the consoles power button or even the Blu-Ray remote then press the PS button on the DS4 after the start screen it auto connects fine, I am using a later Slim model if that matters.