Thanks for reviewing my hack idea! The Fakemon are for a different hack project, not that one...I wanted to do something smaller that wouldn't require so much creation of new graphic/music/etc. material, to practice mapping and scripting for the big one.
You brought some interesting questions to my attention, especially the Pokeball one. Since I wanted to have few or no actual Trainers around, instead scripting battles with wild Pokemon (a la Legendaries of previous games) around and about, I'm having issues with Pokeballs in general. First, how would you get them? Second, how would I keep the player from trying to catch the boss Pokemon (which is a big no-no, storywise)?
Here's my (kinda crappy) idea. I have a character who recurs in a lot of my fanfiction (though none of said fics are posted) - Archimedes the Nidoking. Contrary to his species, he's a scholarly character who, like anime!Meowth, has trained himself in the human language, and is kind of an outcast among Pokemon due to "acting human". In this hack - I think I'll call it Pokemon Cyan - he becomes an ally of yours. We'll say he's on the island...to study the mythology and history of the area. Anyway, he serves as your translator, and occasionally will find you a new ally Pokemon who would like the guidance of a Trainer. Some of these allies - the more common ones, like Magikarp and such - will be provided to you at certain points in the game with little to no effort on your part. Others, like Dratini and Treecko, you have to put in a conscious effort to find, making Pokemon capture into a matter of completing an optional sidequest. Yet others, almost exclusively the lower forms of the Gym Leaders domain kings (Horsea, Scyther, Bagon), are found as eggs through much more challenging means.
This way, Pokeballs are a nonissue, and there's no danger of the player actually catching one of the "Trainers". Sorry for the long, rambling VM...having your advice on this would be great.