Yep, I agree. You're quite right that Jean is the female lead in X3. However, the confusion and debate about who was the female lead arises from the storytelling of the movie. Halle/Storm had a prominent role alongside Wolverine and for a large part of the movie Jean's story was in the background. They also had Phoenix just standing around on Alcatraz. The story structure of the movie was not very good, because the Phoenix plot and Cure plot were not tied together enough and because Phoenix was sidelined for part of the movie.