Well-written fiction is character-driven. Asking your beta reader specific questions about your characters can help you improve them. Characters that seem well-rounded to a writer may fall flat to the reader because of inconsistent writing or a lack of details. Asking your beta reader if your main characters are well-rounded and interesting is important. Ask your beta reader to define your characters' personalities; if he cannot, your characters need to be improved upon.
Stories are constructed with a beginning, middle and end. Ask your beta reader if your story flows smoothly. Ask her if she can follow the plot and if any details confused her. Make sure your story is understandable and clear by asking your beta reader to tell you what the plot is. If your beta reader cannot give you a clear image of your story, ask which parts were unclear or confusing.
Even a perfectly written story will not be read if it does not entertain the reader. Ask your beta reader if your story kept him entertained. Ask which parts of the story made him laugh, which parts made him cry. Find out what your most powerful sentences, details and paragraphs are. Ask your beta reader if he had an emotional reaction to parts of your story where you are attempting to create a strong mood.
Stories have a consistent mood and tone. Horror stories keep us on edge, while romantic comedies make us laugh. Ask your beta reader what she felt the mood of your story was. Point out specific scenes in which you are attempting to set a mood, and ask how she reacted to those scenes. Ensure that your readers will feel the mood you are setting by asking your beta reader to point out her favorite details.