Wait for it
OKay, first off...
As for your idea, to tell the truth, I think it'll work more as an original fic instead of a Pokemon fic. With Pokemon fics, you have to have the basic canon elements in it (the characters, towns, the Pokemon themselves) and not change too much of what's already in the Pokemon world. From what I'm reading, you're actually changing the characters, towns, etc. to make the story fit the plot you wanted. For example, you rid of Pokemon/Pokemon training and have martial arts thrown in. Granted, not all Pokemon stories have to deal with Pokemon training, but that's one of the things common in the Pokemon world and that's one of the ways you're already altering it to have what you want in your plot. I know you already said some events from the game will tie in to this plot, but not sure how that'll work.
And one more thing. I know Gary Stu is a working name, but I advise not to use that name if you're going to make this story a serious one. XD