I've been going nuts trying to get mavproxy.py to work with a pixhawk or navio2. Nothinhg worked, and today I found out there has been a bug with RPI3 assigning /dev/serial0 to /dev/ttyS0, and possibly dropping the baud rate. This has been fixed if you run sudo rpi-update but has not made it into debian yet. I'm sure the erle robotics people know about it already, but its caused me hours of headaches. If necessary I can refind alink to the discussion about this and how it has been resolved. force_turbo=1 and cpu_arm=200 used to fix the problem, so RPI3 telemetry worked for some people. It's now only necessary to put enable_uart=1 in config.txt and ttyS0 should get created and not assigned to a console, unless you want that.