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Believe it or not, I'm actually going to implement this theory as a crucial plot point in the Kanto (FireRed) arc of my (currently unpublished due to still being a draft that's floating around in my head with no way to piece it together) Nuzlocke run. And don't you dare ask any questions about that plot point and how it'll affect the story, because that'll probably just result in the run going forever unpublished. (In case you're wondering, there's going to be four, possibly five arcs: Hoenn [Emerald], Sinnoh [Platinum], Kanto [FireRed] and Johto [SoulSilver], in that order, with the possible addition of Unova [Black or White, depends on which version I get].)
Not changing sig until Knuckles the Echidna wins a Character Battle. When, oh, when will Digimon Xros Wars be dubbed? COLLINGWOOD MAGPIES 2010 PREMIERS WHOOOO!
gbchaosmaster did ask a legitimate question on how an unsubstantiated theory very few people on the internet support can have a major effect on your "fanfic" story.
Besides, the plot "arc" of your story will be chronologically incorrect compared to the game series, as the series goes R/B/Y, then G/S/C, followed by D/P/P, finishing with B/W. The remakes don't count, as that's exactly what they are - remakes.
Where logic won't work - I will PAL Gamers unite - http://www.gamefaqs.com/boards/277-pal-gaming