There are all kinds of angles you can take with an assignment like this, but the two most obvious options to consider are two stories by the same author or two stories on the same subject/theme.  If you are completely open in your choice, then I would start with an author you really like or a story you really like -- one that you would love to research and write about, and then go about finding a complementary story to go along with that.

I think that the stories of Ernest Hemingway would work very well for an assignment like this because many of his stories share the common theme of what is commonly referred to as the "Hemingway Code Hero."  You could research the code elements and then consider two different stories in order to evaluate the main characters in light of the code hero characteristics.  It would probably be more interesting to find one story where the character "lives up to the code" and one where the main character doesn't.  One possible set would be "The Snows of Kilimanjaro" and "A Clean Well-Lighted Place."

Another author that comes to mind is Flannery O'Connor.  Her short stories share many common qualities in terms of theme.  Again, you could do some research about her writing, and then evaluate stories to look for what critics consider the most salient aspects of her fiction.  For example, I would look at her use of violence.  Two of her most famous stories are "Good Country People" and "A Good Man is Hard to Find."  Many of her stories focus on family dynamics.  She is a master of irony. 

If you decide to focus on a single theme in two authors' work, then your options are limitless.  As you read to decide what to use for the assignment, start with something you really like, and then do a search for stories that share that theme.  You  could probably do an Internet search, or post the theme in the discussion board here on enotes and see what other editors can offer you in the way of options.  Good luck!