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.
Consider the idea of spontaneous genesis of life, as used to be belived. What strange kinds of life might arise from modern substances? What kind of vermin would a landfill produce, or an oil spill on the ocean?