Looking through your 'design document', I can't help but scratch my head. You talk as if the game is already done, you've even included system specs, yet... you have nothing coded. How could you possibly know the system specs if nothing has been made yet?
Now from what I could read in this topic, you're planning to be the story guy, the one who's writing the actual story and what not. If so, I have some suggestions for you:
For starters, take some grammar and spelling classes. Take this sentence:
You panic but know that the only way to save your Pokemon life is use what ever
was given to you...
Not only does it sound like something written by an eleven year old child, it is grammatically incorrect that it makes it sound like you are the Pokémon. The entire document is absolutely riddled with these kinds of errors, and if you ever hope to make a game that looks even remotely professional, you really need to watch it.
Other than that... the story seems really incoherent. The boy trainer has a pikachu, the female trainer has a shiny legendary? Why? This makes no sense. Also, while I understand that you like both Pokémon and Megaman.EXE, you're basically just copy + paste two games into one, even though the universes have nothing to do with eachother.
All in all, it feels a lot more like an incoherent fanfic than something that would even be remotely interesting as a game.
Also, I'm just going to leave this here: