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.
What if some crazy wizard created an artifact that empowered rodents that touched it with one random supernatural power? Preferly right out of the pages of your favorite four-color. (But only one power!) This item does not convey any sort of intelligence boost.