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While the odds are incredibly slim, even moreso now that Console and Handheld are combined, I think we'd benefit more from a Third Orre Game, or maybe a new region where Cipher's went and set up base taking advantage of the years of silence after Gale of Darkness.
>while going through old notes Cipher notices similarities between recently discovered Mega Evolution and their Shadow Pokemon, both have their strength drawn out by unnatural causes that can only be lessened or nullified with a strong bond between Trainer and Pokemon
>this ends up giving them the idea to combine the two to bring out the real destructive potential of Pokemon
>they end up acquiring the Regis and many Pokemon who can Mega Evolve
>Shaymin takes up the role of Purifier
>like before, you have a limited variety of Pokemon both snagged and wild but now it spans across all 7 Current Generations
>to make them more desirable all Shadows have their HAs and actually useful moves that can be passed down until eventually the mainline games make those moves obtainable so you don't have a Wish Chansey scenario