" According to an unidentified Tokyo Olympic/Paralympic Committee member, the team behind the ceremony show began preparations in January. This was before Pokemon GO was released. Another reason given was that Pokémon was not as well-known comparatively worldwide. Lastly, the Japanese Olympic Organizing Committee just couldn’t pass up the pun of Mario and Rio from Rio de Janeiro."
And yet they included Doraemon and Captain Tsubasa, which are so well known outside of Japan! I will forgive them for the reason with the pun though.
Link: https://mynintendonews.com/2016/08/26/pokemon-was-left-out-of-the-2016-olympics-closing-ceremony-due-to-international-recognition/
---Member of the official Squeezol Fanclub---