Working with Raspbian Jessie and a Pi 3, version 1.2 (printed on the mother board).
The core problem is that the GPS no longer attaches to ttyAMA0. With the introduction of Bluetooth, it got conflated with the serial port for performance reasons - this may be temporary on new versions. In any case, after installing Jessie, so apt-get update and the GPS should be available on ttyS0. The performance of ttyS0 is slighly less than AMA0, but since it actually works, it's probably a good thing. Still working out all the places, but wanted to record this for now.
Working with Raspbian Jessie and a Pi 3, version 1.2 (printed on the mother board).
The core problem is that the GPS no longer attaches to ttyAMA0. With the introduction of Bluetooth, it got conflated with the serial port for performance reasons - this may be temporary on new versions. In any case, after installing Jessie, so apt-get update and the GPS should be available on ttyS0. The performance of ttyS0 is slighly less than AMA0, but since it actually works, it's probably a good thing. Still working out all the places, but wanted to record this for now.
Reference - http://spellfoundry.com/2016/05/29/configuring-gpio-serial-port-raspbian-jessie-including-pi-3/