Ah, I worded that badly. Ultimately the pilot is the decider as you say. I was getting at the idea that (so I am told) the day to day experience of piloting is very much about working within a regimented system.
Strongly reglemented: yes; however, the rules are cut out in a way that requires _a lot_ of due diligence and experience to make sound decisions. For instance, EASA rules so no problem whatsoever dispatching an aircraft with minimum fuel (fuel planning regs) and no alternate planned (alternate planning regs) towards a destination that has thunderstorms in their weather forecast (weather regs)... it is up to the flight crew to mentally "fusion" different regulations together and make sound and safe decisions.