1. Would the story in the Anime be different than in the Manga? The exact same? Or the same with a few fillers and extra stories?
Nintendo would make Pikachu a major character. When making the current anime, they realized that Pikachu was easy to market, and told the animators to give it a large part. If the anime was based on Pokemon Special, the same thing would have happened.
3. Who would handle the dub and how would it be handled for US distribution?
Probably the same people, and it would still get Americanized/censored. Nintendo wasn't sure the franchise would succeed outside of Japan; there hadn't been many successful anime/RPGs. They made the changes to ensure it's success.
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