PokéBase - Pokémon Q&A
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Well, Pokemon, as one would expect, is influenced by Japanese culture. The shrines also tend to be associated with legendary Pokemon, like celebi or landorus, who have great influence on nature and spirit. Similarly, in Shintoism, moderately sized wooden structures are built to enshrine kami, spirits of great importance in regards to spirituality or natural phenomena. As such, the presence of shrines in the Pokemon games is likely influenced by or a homage to Shintoism. There are likely other sources of inspiration in addition to this.

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ugh...your answer is better. +1
also notice that landorus is part of the KAMI trio
Yea, you get an up vote.Thank you for working so hard to explain my question!
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Because Game Freak wanted to make it so there is always a place to worship Arceus.

Seriously though, the main reason seems to be little more than atmosphere. It feels like home when you enter your Pokemon game and there is small shrine dedicate to the keeper of the forest. other than that, there is no real reason. Often, legends can be found and caught in these places, such as Landorurs in BW.

Hope I helped x3

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