Raspberry Pi 3 connecting to Pixhawk

[fnoop]

From my link above:

@fnoop

Hi, pi3 has changed the uart access a bit because of the onboard bluetooth. In short, you need to disable the onboard bluetooth and reassign the exposed uart gpio back to the PL011 which has better timing at different clockspeeds. It’s then accessed as before on /dev/ttyAMA0.
Add this to /boot/config.txt:
enable_uart=1
dtoverlay=pi3-disable-bt

Also make sure to disable (0) BRD_SER1_RTSCTS or BRD_SER2_RTSCTS depending on the telemetry port you’re using.