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Don't forget the Red Gyarados event broadcasting on TV in Sinnoh at the beginning of DPPt. Unless there were two separate shiny Gyarados that both appeared at the Lake of Rage, GSC and DPPt both take place at the same time. The Fairy type and Mega Evolution being "newly discovered" indicates...
I'd like PokeMarts to be kept separate, for convenience's sake. If we're keeping customization, the areas where they used be could be replaced with either normal houses or Boutiques, depending on the town.