Starting in Pocket Monsters Best Wishes, the anime began using another new made up language to obviously reduce the costs of paint editing the show in the various different languages that it is now distributed in. Originally the series had Japanese text and it was painted out by the English dub. Later, a made up language debuted in the Orange Islands but it did not show signs of it being a distinct interpretable language.
This new language that is used in Best Wishes is actually a simple substitution cipher where one basic modern Latin alphabet letter is replaced with a symbol from the made up language. Thanks to all the people in chat that helped out deciphering the symbols. Serebii suggested I post this here as its very interesting in regards to the anime series.
Link to Chart: http://www.pocketmonsters.net/Anime_Language
Link to Imageboard thread of instances: http://www.pocketmonsters.net/ib/threads/2708
We are also looking to find all instances of the Language as seen in the anime. If you know of episodes that have the language, please post the episode number, the time index / or quick summary of the approximate area it aired in.