On many large RAF aircraft the pilot is merely the driver, and the "tactical aircrew" are often more senior and/or responsible for the "mission" and so make those decisions and direct the pilot as to what is required of the aircraft. The safety and flying is the domain of the pilot. I think "captaincy" and "mission" are too different things, but the pilot is the man flying. Interestingly how things have changed in that higher levels of leadership were the sole domain of pilots but now "back end aircrew" fill many of these posts. On helicopter squadrons I have seen navigators as the squadron commander - but there is no requirement to have a navigator on a helicopter, but we had so many left over that you had to do something with them! With the rise of health and safety and risk management you need specialist engineering skills to determine if an aircraft is fit to fly, often the pilot does not have the knowledge or information to make that call. He always makes the decision to fly but he may not always get the choice.
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