I've been bothered by this film for about 15+ years, all I can remember is the ending.
The film takes place on a flying boat/ship. It was big and had sails and was made of wood. It used smoke effect clouds, I don't think a lot of CGI. The main character is a girl, trying to find her father or young teenage brother, I know they are both in it.
There is a crew that fights a lot. At the ending it's the boat waiting to leave, at a dock, lots of smoke, love interests and a choice to stay or go. Someone chooses to leave with the boat, because I think they will forget once they go back to their normal lives and they want adventure.