There are all sorts of opinions on rules, house rules and how they interact with the play style of a RPG. I know people who hate house rules and I am their bane (as I've discovered in the game I'm currently running.) I LOVE house rules - before 3rd edition D&D came out we were playing by what my friends called "Chad Edition". Combat was almost completely redone with Armor Values, fighting modes, initiative tracks instead of rounds and all sorts of other custom madness. I saw the Player's Option books as toolbox to build something that matched my vision. And 3rd edition along with all it's d20 additions was the grandest toolbox of them all.
Part of this is probably a symptom of having not played a lot of different game systems growing up. Up until college it was D&D of some form and DC Heroes with the occasional Marvel Heroes or Gama World. In college I expanded into the Storyteller system but didn't really mess around much outside of that. In short I had a very limited tool set to run games with.
One consequence of this is that when thinking up a game to run I didn't think to myself, "I want to run a game of 3rd edition D&D!". I thought, "I want to run a fantasy game in a world that feels like Diablo!" I then came up with the general setting, adapted the d20 rules to work with that vision, readjusted the setting to the limitations of the system, readjusted the system to fit things even more, etc. It was a laborious task, usually. This is probably why I have so many notes - lists of world notes followed by the needed adaptations to the system.
Sometimes the adaptation went the other way. A lot of my d20 settings come from seeing cool ideas that relate to each other across different products and trying to pull them together. Like taking all the shadow related d20 materials (Shadowcaster, Shadowdancer, Pnumbral Lord, that shadowy school in Bo9S) and tying them together in an organization. This was probably expressed the best way in a game I did run once where there were various guilds that determined which feats and prestige classes would be open to a character. Hell, even though I'll probably never use it I find myself expanding that world out to be even bigger and better now.
But all that is mostly for how I used to run games. As I noted, the things I write about in this blog are from old notebooks. Now if I actually want to get a game played I need to grab a system and just run it as it intends itself to be run. Start a game of Dungeonworld and just go with the flow like it says in the book. But I still enjoy the old way of doing things. I picked up the Radiance RPG purely because it incorporated a lot of the d20 house rules that I love but I have little desire to run it in the world or style it was probably meant to be used for. I think the game was meant for a more urban and civilized type of game. My first thought was to use it for a hexcrawl through abandoned steam and electro tech ruins.
I guess the point of this post is to let you know that there will be house rules as usually the world was imagined first and then I just used whatever tools I had available to bring it to life. I hope they don't make you cry.