I don't know about an outright adult-oriented Pokemon story, but the potential has always been there for a more mature one. Just look at the direction Digimon went especially with a series like Tamers. My biggest criticism of the Pokemon franchise has always been that they shied away from ever having a more fleshed out story or exploring darker themes, in either the anime or the games. Several of the games have a nucleus of a good story but they feel held back by the fact that the villains and threats feel a bit too Saturday morning cartoon esque
The thing is it'd be weird to do it now, and would come across as "cringe" (That dreaded word), because everyone is used to the Pokemon they grew up with which is a traditional light-hearted Nintendo series.. Whereas Digimon started from series 1 with plotlines that featured major characters getting literally killed, cities being levelled, global disasters, "glowie" type figures behind conspiracies, etc. Pokemon COULD have gone that direction as well, particularly in Gen 1 (the original lore and artwork of which gives off this sci-fi vibe with weird experiments going on, and an emphasis on Mons being actual "capsule monsters" rather than just animals), but they chose not to. It'd be hard to go back on that now without it getting labelled as overly edgy or grimdark or whatever.
Also, what about Colosseum? I loved that game and think it captured pretty well what a slightly darker Pokemon game could look and feel like. Too bad Game Freak seem to have some grudge about never revisiting the Orre region (and maybe don't even consider it canon as it wasn't their game).
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