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"Gen 2" as it is known, produced the single worst mainline entries Pokemon has ever seen. Johto games are consistently lazy and painfully uninspired. The entire region is a listless rehash of the Kanto region, and this permeates everything. Johto reuses Kanto's league and premise and even has the same narrative beats. But instead of a thrilling climax with Silph Co. and Giovanni's gym, Johto's storyline whimpers out following the seriously uneventful "raid" on the Radio Tower, if one could even call it that. Then, to make matters worse, instead of opening up more of Johto so that it could potentially develop a stronger sense of identity, they just stop trying altogether and take the player back to Kanto, which would have probably come as a relief to the die hard Pokemon fans of the day had Kanto itself not been severely abridged. The game tries to justify Kanto's ramshackle state as a product of the passage of time, but nobody's buying it.
Outside of things like the Day/Night cycle, which nobody asked for, and Dark/Steel which were good additions, GSC added almost nothing of merit to Pokemon as a franchise. Pokemon as a whole would probably have been better off without GSC, as more development time could have been spent on RSE, which, considering how progressive they were, are more deserving of the "Generation 2" title than the actual Generation 2 games. HGSS had the chance to redeem Johto but it fixed almost nothing but the terrible Pokemon distribution, and then tried to patch up its shortcomings by aping off of the Sinnoh region, just like it aped off of Kanto back at the turn of the millennium.
It's baffling to me that the Johto series of games have a fanbase at all, let alone one that has the audacity to call them the best. It's the biggest case of mass hysteria I've ever seen in my life. Make no mistake, GSC killed Pokemania and left the franchise as a whole treading water for fourteen years.