There are two ways: 1: get Mission Commander (MC) and press ‘clear callsigns’ on the Pilots tab (after loading the save offcourse). 2: Also in MC: change individual flight callsigns by opening a flight and in that sub-window you can select a specific callsign (kind of self explanatory).
There is always room for improvement, but after listening to all those numbers they (AI) call out on the radio, I am always pleasantly surprised at how natural and conversational it sounds.