What Could Have Been: The beta screenshots and known beta video for the game look vastly different from the final product.
The game was originally for the failed Nintendo 64DD. A video of the beta can be seen here.
Also, the game was originally planned to be just a generic picture-taking game.
Ekans was planned to be in the game, which would have made the final total number of Pokemon 64.
There was once a music track called "Fantastic Horror" found on Ikuko Mimori website. This suggests that there may have been a level centered around ghost-type Pokémon. This may have been scrapped because there were only three ghost-types in Generation 1.