Plagues and other great diseases are important parts of history and some settings. They defy man and may even defy God in their swift and terrible punishment upon the body of society.
My issue with modifying/removing dwarves and elves is that the PC’s may want to play them.
One of the most powerful tools found in the World Building 102b article is the Worksheet. Here is a place to put the settings you might make with them.
Atheists and agnostics get a jolt when one or more deities make an appearance, and take a direct interest in things. It is hard to deny the existence of gods when one has met them face to face.