I guess Fuu is the main character of the show. After all, she's the only one to see any true character development so far. Mugen and Jin are just along for the ride.

Of course, that's a bit interesting in itself. What do Mugen and Jin have to gain from accompanying Fuu on her journey? Obviously, they care enough to protect her every time she finds trouble - which is often. But why?

Cowboy Bebop traveled a similar path, with a group of characters that, despite being linked only by circumstance, couldn't leave each other alone. They were responsible to each other, yet rarely owned up to it. I see the same in Samurai Champloo.