Copter-3.6 supports both mavlink1 (the default) and mavlink2. mavlink2 is backwards compatible with mavlink1 though so very few changes are required on either the ground station or ardupilot side.
One change that needs to be made to use mavlink2 is to set the SERIALx_PROTOCOL = 2 for all UARTs that will try and speak mavlink2. So in particular, those connected to telemetry radios.