1) It's a Space Ship, when the ship is in Space - where I would assume it spends most of its time - that section would be open to space. The point of a giant, canyon-like gap in the middle of a spaceship is beyond me.
2) Those things you dodge aren't all supply-crates, they're large structures that are a part of the ship, and as such make no sense whatsoever. It's like that move 'Galaxy Quest', when these two people have to get somewhere, and to do so they must go through this completely arbitrary series of obstacles.
3) Yeah, the whole distance thing is kind of cookey, but it is entirely reasonable when you consider the fact that the cutscenes used the in-game engine, and as such they couldn't very well make the ship 4 Kilometres long while keeping a sane loading time.