Create your three-act structure. Regardless of length or medium, good stories generally follow a three-act structure. The first act introduces the audience to the characters and the world in which they live, including the physical rules of that world. This is particularly important in an animated story, where animals talk, main characters fly, and anvils cause minor head injuries. The main character encounters greater and greater challenges throughout the second act, until she reaches a moment where she faces utter defeat. And in the third act, the main character overcomes all obstacles to achieve her goal.
Focus on your timing. Three act structures are typically tight affairs, time-wise. In a traditional feature film, the first act lasts about 30 minutes, as does the third act. The second act can last anywhere from 30 minutes to one hour or longer. Follow the same convention for your animated pilot and split your 10 minutes into thirds, giving each act three minutes to play out (give the second act the extra minute).
Nail your plot points. The end of each act should spin the story in the new direction. This moment is often called a "plot point." At the end of the first act, something should happen that sets your main character off on her journey. If she's a mouse, perhaps a rival cat has stolen the cheese that will feed her family. She must get it back. At the end of act two, the main character faces her greatest challenge, all looks bleak, but she finds new resolve. The cat catches the mouse and prepares to eat her, but she finds a way to escape at the last minute. The biggest plot point is the climax, and it comes at the end of act three. This is where the main character's story is resolved in great fashion. Think fireworks finale. The mouse defeats the cat and discovers a fortune in cheese -- enough to feed her family forever.
Make your story entertaining. This may seem subjective, but there are simple steps you can take to make sure your story is compelling to audiences. The biggest rule? Show, don't tell. An animated pilot is, at its heart, a visual story that must capture the audience's imagination. Your characters should act rather than talk about acting. The mouse should battle the cat, not return home battered and tell her family how she fought the cat. Challenge yourself to write a story without dialogue, as dialogue can be an expository crutch. This exercise will help you tell more compelling, entertaining stories.