Two things very wrong
I liked the animation style and everything although the story was cliche. I really thought the boat was original. However, one glaring problem is that the Syndicate are no threat whatsoever. They have no weapons, except one guy has one gun out of eight it seemed, they have no fighting skills, and they are completely incompetent. If I were living in that world, I wouldn't be scared at all. These guys aren't even thugs. They're hobos. Yet the girl is afraid of them? I didn't buy it.
The second thing is also a big problem. The girl's eyes are way too big. I know it's the anime style, I've seen enough anime to know, but every other character in the movie had normal (or relatively normal) proportioned eyes. Hers took over half of her face. You need to tone that down. It just makes her look silly and when I see her, it makes me think of the artist style rather than a legit character with emotions and thoughts. I'm not thinking about what she's saying but I'm enormously bothered by her hideously freakish appearance. She's a freak, not a character.