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Masuda said in an interview he doesn't want to change the cries to match the anime and he thinks they should be separate.
Many of the cries in-game are exactly the same audio file but just pitched up or down or mixed differently.
Inside the Pokemon game there is actually an in-built mixer. Audio files are some of the biggest space-takers in a videogame so it's smart of them to only use a handful of audio files for the cries and then make them sound different using the mixer.
If you rip the data from the games, you can actually find the beta GUI for the mixer (Pic related) they use when testing the cries against the DS speaker hardware.
The idea is to make the cries different sounding enough using only the mixer so that they sound noticeably different through the small speakers on the DS hardware.
