First, it should continue to develop a student's technical skills.
Second, it should be a kind of creative crucible -a production which incorporates the previous years of study and pushes concepts against practicality.
It's not unreasonable to expect a 2:00 film to be produced. The bulk of a student's credit hours should be dedicated to producing the thesis film. 6 class hours a week. Here a student will learn professional production practices.
Continuing to develop animation skills, we'd use Richard Williams' "Animator's Survival Kit" as the final year workbook. By this point a student should have a basic grasp on animation mechanics, making the advanced studies in this book useful.
This is also the time to start developing as filmmakers. There are two general film resources which are invaluable.
Steve Katz' "Shot by Shot" and John Sayles' "Thinking in Pictures".