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you can connect rasp pi with pixhawk via telemery port. and i have hardware for make it easy!
im wondering if you have had any luck with your problem? i am also using pi3 + pixhawk (using the above recommended cable with the wires swapped as per the ardupilot guide), serial ports are off. im getting almost the exact same thing as you although i dont get "Waiting for heartbeat" just "MAV>" entering commands like "param show ARMING CHECK" does nothing... just gives me back "MAV>"
by the way how do check the baud rate on the pixhawk? pretty sure its set to 57600 but i wanted to check.
hope you dont mind me joining in but i figured if were running the same companion computer and having the same issues we might be able to help eachother out!
Yes I still get the same problem. I have even tried it using two linked telemetry radios. All I get is
pi@raspberrypi:~ $ sudo -s
root@raspberrypi:/home/pi# mavproxy.py --master=/dev/serial0 --baudrate 57600 --aircraft MyCopter
Connect /dev/serial0 source_system=255
no script MyCopter/mavinit.scr
Log Directory: MyCopter/logs/2016-04-30/flight20
Telemetry log: MyCopter/logs/2016-04-30/flight20/flight.tlog
MAV> Waiting for heartbeat from /dev/serial0