I feel like a lot of people kinda miss what the Johto games were going for and have their judgement too clouded by the design philosophy of future games.
The fact that every Pokemon game starts with a cursory introduction to the world of Pokemon by a professor, hell the fact that there's a professor present in the games at all, is kind of taken for granted nowadays, but back then the whole idea was that these games revolved around the research and discovery of Pokemon.
Battling was a part of it obviously, but it was a means to an end - you needed to battle to get further into the region where more Pokemon dwelled - it was never your main goal, your main goal was completing the Pokedex. Hell in Red and Blue nobody tells you anything about gyms during the game's first hour and your rival never really gloats about gym badges at all, it's all about the Pokedex.
Which brings us to Gold and Silver and the way it handled the inclusion of its new Pokemon, where the idea was to put a lot of them in weird, obscure out of the way locations so that it'd feel even more rewarding when you found them - an actually rare Pokemon that nobody else in the game has feels like a true discovery, which is what Pokemon was all about back then.
Red and Blue didn't have any rumors of secret boss fights, but it did have tons of rumors of where and how to catch new kinds of Pokemon in really obtuse ways, which is what GS played into.
These fan team reworks giving every gym leader new Pokemon - especially stuff like giving Morty Misdreavus, one of the rarest Pokemon in the game - just robs the game of that sense of discovery.
