Adjust the registers in the room where too much heat/cooling is present so that the registers are partially closed. For example, to get more heat upstairs during the winter, close the registers downstairs to force more airflow to the registers upstairs.
Another possible solution is a furnace equipped with a variable speed blower motor. These furnaces are designed to overcome airflow problems and keep the airflow steady throughout the entire house. These types of furnaces can also save money in operating costs.