When I first watched Howl's Moving Castle about the time it came out, I didn't like it that much. It was also one of my first Miyazaki films.
Having seen a few more of his, there's still pacing issues, but it has improved in my eyes. Even in a few of the characters are skimmed over (Turnip Head), the animation is gorgeous, and it's perfectly watchable only for that. If you're looking for Miyazaki's best though, look to his other work.
It was really weird to me when people would say they didn't understand Inception, but if they saw it again, they'd probably get it. It's not a hard movie to understand. The only truly confusing part is the first thirty minutes, but once Cobb explains everything to Ariadne, the audience proxy, it's not hard to follow at all. Every part of the movie's logic is explained at least three times, which becomes detrimental to rewatches.
The Prestige is less easy…
I've never listened to any of Daniel Johnston's music, but this documentary puts you in his head and doesn't let you escape even when the demons come. You see the people who inadvertently hurt him and the people he inadvertently hurt. You see a musician's descent into madness. It's heartbreaking at points. I don't think there's anything sadder than seeing a father crying because he doesn't feel like he can do anything to help his son. But it's heartwarming. It's the story of a deeply troubled musician, but it's a story of love too.