Initially, there were meant to be 9 Gyms in the original Red and Blue games. We all know how Sabrina's Gym is located right next to the Fighting-Type Dojo in Saffron City, right?

Beforehand, the Dojo was originally meant to be a Fighting-Type Gym and the two gyms were meant to be mortal enemies, always battling to see which would be part of the official Indigo League. In this beta version, you had the option of which Gym you wanted to face. 

The Gym you chose would determine which Gym would be entered in the official Indigo League. So, if you chose Sabrina's Gym, her gym would be entered in the line-up of Indigo League Gyms. If you chose the Dojo, it would be added to the line-up of Indigo League Gyms.