Are there any other networks to be found besides your own? In my case, the scan finds about 5, including neighbors and across the street, and sometimes a coffee shop nearby...
What I am getting at is, if for some reason the Pi cannot communicate with your wireless router, can it at least see some others?
Also check to make sure your network is not set to "invisible". That can make troubleshooting difficult.
edit:
Oh, and btw, I only own a Pi 2, so some of the Pi 3 bugs (I mean features...
) are above my paygrade, and someone else may have to pick this up.