I completely agree with the idea that the gaming system should mesh with the intended setting, but in my experience, it is difficult to have complete freedom as a GM when the eventual setting is going to be inhabited by your players. In my time GMing (about 6 years), I've noticed that my players tend to resist systems that lack advancement in the form of levels. Myself, I prefer a point based system, e.g., Shadowrun, Tri Stat or the Storyteller System, but when I present this to my players, they seem hesitant to abandon their preconceptions about levels and rolling high on 20 sided dice. Maybe this says more about myself and my players, but I view the the gaming system as a link between the players and the game, so when I find myself with players who need a square peg and a game that needs a circle one, I usually have to go with the "more accepted" d20esque system.