I havent tried messing with supply/resource/income settings yet but I do recognize that they have the ability to create a different game with different strategies. I will probably get around to them eventually.
I sometimes set indepts higher. And sometimes even lower (which makes a VERY interesting game on a mega-map).
I do tend to set magic sites higher in my own games. I might eventually get a script done to push the magic sites to the max and beyond (read bit-binary terrain settings and up it on the map).
In case people havent noticed, I have a strong tendency to head off in any direction that the crowd isnt going. With so many options in this game, I get peeved at the impression that certain strategies are game-killers when they tend to be strong strategies only for certain game settings. So I love to explore the options and see if it might make a playable challenge.