Yup to you both!
Nagasaki...
1. Actually, I was hoping for some heavily-armored samurai opponents, some sword-versus-gun action... some showcasing of exotic Western military hardware, you know?
2. If the characters spend twenty-odd episodes trying to reach Nagasaki, they should spend some more time there, taking in the atmosphere and getting into some kind of minor scuffle before the final showdown. There should be a surreal feeling when a long trip finally concludes--where was it?
3. It could've made a great nexus for the consequences of all the trio's actions.
The Dutch traders could have made another appearance... the ninja-girl, the abused wife, the Ainu... the people that the trio passed, the organizations their hijinks smashed... some could've come back near the end to either help or haunt the trio. Then there wouldn't have been a filler-factor!
Champloo had so many great moments, but since so many of them had so little overall importance... I hardly remember most of them.
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It's a shame when there's a great show with just one movement, just one cast of characters--in Champloo's case, the trio making it to Nagasaki. I think the perfect plot allows for some characters to come and go, and for new objectives to arise, without feeling arbitrary.
I watched Paranoia Agent before Champloo and I enjoyed how the plot completely shifted direction at episode five, then again at episode twelve, and still connected everything together! So dense! Paranoia Agent's writer, Satoshi Kon, wisely kept it down at thirteen episodes.
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Anyway I think we can all agree that Champloo has a quality of animation surpassing even Bebop, maybe... even FLCL...?
The ride was fun and classily done. I'm very glad I watched it.