Here are a few quick tips I have:
  • Accept Imperfection: Both your own (not everything is going to make perfect sense) and that of the actors in the world. People will make bad decisions and miss "obvious" things for generations. It has happened before it will happen again.
  • Accept Contrivances: If you have to make sections of the map overlap with other worlds so you get creatures that don't exist anywhere else than do it. Especially if you fold them into the setting's premises and let those effects be felt it can work better than coming up tones of individually more natural solutions.
  • Cut the Cruft: Don't include things that don't fit the setting, you don't want to deal with or you don't have any ideas for.
  • Think about Interactions: This really helps things feel more natural and also solves the whole "there are 6 things that could have ruled the world" problem in that they can kind of balance each other out.
  • Remix and Adjust: I don't think I have ever written a setting where elves took a hundred years to grow up because... that's really hard to actually work with.