A lot of information has leaked about the development of Pokémon Gold & Silver over the past two years and it's clear that the game went through a number of iterations before the creators were happy with the final product. One of the mysteries that has cropped about the Johto region involves Game Freak's original plans for the Elite Four, as the line-up went through different revisions over the course of several years.
In 2018, an early demo build of Pokémon Gold & Silver that was exhibited at Space World '97 leaked online, revealing a very different vision of the game. Since then, a number of early development builds of Pokémon Gold & Silver have been uploaded to the Internet. These demos contained sprites for a number of unused characters & Pokémon, as well as early renditions of familiar faces. The Elite Four gradually changed over the development of Pokémon Gold & Silver, with only one familiar face remaining in the line-up the whole time.
Version 1 - Misty, Bruno, Lorelei, Giovanni(?)
The Space World '97 demo of Pokémon Gold & Silver had a radically different line-up for the Elite Four than the one from the final version of the game. According to the internal data, the Elite Four consisted of Misty, Bruno, Lorelei, and Giovanni.
Misty's inclusion in the Elite Four can be explained by the fact that the Kanto region wasn't intended to be a major part of the game. The original plan for Pokémon Gold & Silver was for the player to travel all of Japan and for Kanto to be reduced to a single city. As such, the player wasn't originally going to be able to return to Cerulean City. When Johto was turned into a region and Kanto was expanded, Misty had a role as a Gym Leader once more.
Bruno is the only consistent member of the Elite Four throughout each build of the game, even though he was the easiest one to take down in Pokémon Red & Blue. Lorelei remained part of the group for a few more revisions and was a serious contender to remain in the game, but she was eventually replaced by someone else.
The last member of the Elite Four has been called into question, but Giovanni is listed as a member of the team in the internal files of Pokémon Gold & Silver. He is referred to as an Elite Four member, but he isn't placed next to the others in the internal listing. As such, many fans believe that this was a result of a mix-up. Giovanni was planned to appear in Pokémon Gold & Silver during development (his overworld sprite can be found in the Radio Tower), but it's not 100% certain that he would have been a member of the Elite Four.
Version 2 - (Agatha Returns & Lorelei Turns Into Karen)
In the later builds of Pokémon Gold & Silver, it seemed that there was an effort to bring back the original Elite Four. Agatha could be encountered in the Space World '97 demo of Pokémon Gold & Silver, but she had no trainer data. In the later builds, she was brought back with an entirely new sprite.
It seems that Lorelei was seriously planned for a return to the Elite Four. There are several different unused sprites for Lorelei, all of which use different poses. One of these poses is very interesting, as it's almost identical to the one used by Karen in the final version of Pokémon Gold & Silver. It's possible that Lorelei was intended to be the final member of the Elite Four, but she was replaced by Karen at some point in development. Pokémon Gold & Silver lacked any major Dark-type trainers, even though the typing was introduced in those games. Rather than reusing a character from Pokémon Red & Blue, Karen could have been brought in as a late replacement and her design used Lorelei's pose as a base.
The Elite Four In Gold & Silver (Will, Bruno, Koga, Karen)
The final version of the Elite Four was a mixture of new characters and familiar faces. Bruno survived all the way through the development to make it into the team and he was joined by Koga, who served as a Gym Leader in Pokémon Red & Blue. The new members included a Psychic-type trainer named Will and a Dark-type trainer named Karen. Misty remained a Gym Leader, while Agatha, Giovanni, and Lorelei never appeared at all in Pokémon Gold & Silver.
Source: The Cutting Room Floor