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.
A little way up the narrow valley, before they reach the woods, the PCs notice the squat, tumbledown buildings by the riverside. They are hardly big enough for a human to stand in, and the complex cogs and shafts that occupy the central cavity of one of the buildings are perplexing. What were these buildings? And how safe are they to explore?
Alternatively a desolate place is the perfect setting for a derelict chapel or croft. There needn't be any actual physical encounter involved, but it adds atmosphere to a place to see its dead history. For instance, in the Outer Hebrides there are whole deserted villages which were razed to the ground by the English during the Clearances. Such stories give a setting authenticity and character.