This problem is not uncommon in Japanese animated films. The biggest problem with the plot is that it raises so many questions and then answers so few of them. To be a decent story most if not all of these questions should have been answered in the writer's mind. Only one of those questions is answered and not really very well. At under ninety minutes the film does not seem to have time for explanations.
General opinion is that the actual animation techniques in Japanese animation is very good.
That very simply is not true. It is a lot better than bad Saturday morning animation. I think what people are responding to is not the animation techniques, which are primitive, but the art direction which actually is quite nice, though it does not stand out from other anime films. Oddly, the song over the end-credits begins in Japanese and then lapses into English. But for a little bit of fancy editing, this could be a TV movie from the 1960s.