I see, that's very interesting. Do you think the Ruins of Alph and the Sinjoh Ruins are related? What kind of relation would they have?
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Silktree
It's explained in HGSS that the Ruins of Alph clan had to leave Johto to protect the Unown, and at least some of them helped build the Sinjoh temple.
Blast
Is that so? I never knew. It might be possible the humans felt like they were harming the Unown by forcing them to do their bidding and that's why they left...
Conservative theory: The clan that built the Unown temple wanted the Unown to draw powers from ancient Pokemon in order to teleport to the Pokemon world.
Ambitious theory: The clan wanted the Unown to create those Pokemon, which had only been a figment of the imagination. Perhaps the Unown also created Mew, and in turn, every Pokemon.
Bear in mind that the second theory isn't supposed to be consistent with anything but the first two generations.