Getting better. Still, however, it feels like you are creating plot elements to fit your mold, rather than the plot driving the story. It's kinda like you went, "Okay, so I need a reason for the guy to be evil. I know!" This isn't always bad, but it's best to avoid this process, especially if we can pick it out right away.
How about that the evil man, is evil and want's to rule the world he lives in, because in his childhood, he was the one serving the highest ranked people. His parents where killed in a riot against them, and all orphans were to serve for the highest ranked. But then one day he escaped from them, and created an army of cyborgs, and went against the people who had used him in all these years.
The crystal with the great powers was only a myth, until one day, when his soldiers were on a routine check around the villages, they caught a girl that had the crystal around here neck. In a necklace. If the evil man could get a hold on that crystal his powers would be amazing, and no one could stop him.
The girl was told, when she got the necklace from her dying mom, that when ever she was in danger, she should simple just take the necklace, and say "help" and then throw it against the sky, and it would get help. The necklace would find the best suitable person to help her. In this case it ends up with our main character which name is Daichi. And it's kinda ironic because Daichi is not the adventure, brave, fighter kind of guy. He is like the oppisite...