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The "edgiest" the series has ever been was Pokemon Colosseum, and it was pretty refreshing !
>MC's from an evil team
>Stealing pokemon mechanic (Even though you technically snatch them back)
>Shadow Pokemon
>Ultra mode that made your pokemon directly attacking you
>Overall cool desert/desolated map
You don't need to go all "mature rating" to set a more serious Pokemon game. I wish they would do a game like Colosseum and its sequel again, but it won't happen.