Not bad, you have improved. Your original characters are a little more well-developed, and your grammar's improved a bit. The plot makes more sense, at least by Pokemon standards.
What you have to do now is work on the slightly more advanced stuff, like dialogue and description. Try reading some professional fiction novels, a good sci-fi, fantasy or mystery, and see how they do it. Also, I'd like to recommend an author called WatsonSword. He writes for Lilo and Stitch and Digimon, and maybe some other fandoms. His fics that I've read are probably the best I've seen on the site. Gems of Tomorrow and Empire of the Pacific, both Lilo and Stitch fics, are worth a look. Gems isn't finished, but Empire's a bit darker, so take your pick.