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So originally, Game Freak was going to make a game called Capsule Monsters. They couldn't get the name trademarked because of Capsule Kaiju from the Ultra series, which they were based upon. So instead they went with Pocket Monsters, or Pokémon for short. Miyamoto suggested splitting the game into versions to encourage trading and interaction. The original version ideas were Red, Green, and Blue, but they decided just Red and Green were enough. They started work on Pocket Monsters 2 immediately following the completion of Red and Green. Then they blew up in popularity and so Game Freak decided to officially announce it and Ho-Oh in July 1996. CoroCoro wanted to capitalize on the success of Pokémon and got their own exclusive version commissioned, which was called Blue, to be sold through their magazine. Pocket Monsters 2 was renamed to Gold and Silver, but there were frequent delays. To keep up brand momentum during these delays, Pocket Monsters Pikachu (Pokémon Yellow) was released in September 1998 in Japan to capitalize on the popularity of the anime. In November 1999, Gold and Silver were finally released. However, one month later, Nintendo announced the Mobile Adapter GB and that they had Game Freak making a Pokémon game that utilized it, codenamed Pocket Monsters X. This was Crystal.
TL;DR - The original vision for the franchise didn't include split versions, third versions, or Yellow. It was only in Gen III where it became increasingly obvious that a third version was planned from the start with Rayquaza. We could have simply had
>Capsule Monsters
>Capsule Monsters 2
As the first two Generations. But had development gone smoothly for the second game, it would have been a regular Game Boy game with SGB enhancements.
Masuda said during Gold and Silver, he had plans for Ruby and Sapphire, FireRed and LeafGreen, and Diamond and Pearl as the ultimate Pokémon games.
