Free Willy 3 is primarily about Max, an intelligent, inquisitive ten-year-old who accompanies his father on a whaling expedition. His conscience bothers him about his father's career, but instead of taking the usual route of performing a string of silly pranks (like you would see in a lot of children's shows), he tries reasoning with his dad. He also asks question after question -- not just about the technical aspects of whaling, but he also delves deeper into the more important questions of life ("Do you always have to do the right thing, even if it hurts?").
One of the things I liked best about Free Willy 3 was the realistic and sympathetic portrayal of the father, even though he was the "villain" of the story. He was a man doing a job that has been in his family for years, and without it he wasn't sure who he was. Despite having a career others disagreed with, he was a caring, compassionate person who loved his son. Other characters are drawn out nicely as well -- Jesse and Randolph, from the first two films, and their new co-workers on the sea -- showing their tempers as well as their more positive sides.
Couple all these features with stunning cinematography and a beautiful score, and you have one fine film!
