Probably many people find the story confusing. I felt the same way when I saw it in the theater for the first time! The story seemed arbitrary and I couldn't connect the pieces together (much like I saw "Ashes of Time" for the first time). But when I watch it again on the DVD, I realize the movie is probably about one thing: personal freedom.
Howl is a free person. He doesn't has a heart and even his home (which is usually characterized as a stable point in one's life) can move :-) He is disguised as different wizards in different counties, and when Sophie asks him how many identities he has, he said "Enough to guarantee my freedom". When Sophie confronts Suliman, she comments Howl as "selfish and cowardly and unpredictable, but he's straight as an arrow. He only wants to be free." But in Miyazaki's world, nothing is black and white. According to Suliman, Howl's power is too great for a person without heart, and he will eventually becomes a monster (some political figures come to my mind).
Sophie, on the other hand, is bounded by responsibilities. She is young, but her heart is old. She refuses the invitation from her friends and keep working at the hat shop. When her sister asks her "Are you going to spend your life in that shop?" She replies "It meant so much to papa. Besides, I'm the eldest.". Even her sister asks her to "look out for yourself". When Sophie is turned to an old lady, it actually set her free because the good thing of being old is that one has "so little to lose" She becomes more adventurous and takes control of her life. She is very assertive as being the cleaning lady in Howl's castle and even tames Calcifer to cook her food. For Howl, his turning point comes when he refuses to move his castle anymore (I'll leave it to the reader as why he does that) By the end of movie, he regains his heart. He feels terrible because it is like "trapped under a stone". And Sophie says, "Yes, a heart is a heavy burden".
There are other wonderful things in the movie. For example, this is probably one of the few movies that tell me what it is really like to be old. But I do want to highlight the thread about personal freedom as it will help you to tie up the pieces of the story.
Since there are 1000 words limit in the comment system, I'll write more in by blog: http://web.mac.com/kenlaw/iWeb/Site/Blog/Blog.html