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>nonlinearity forced a shitty level curve
>poor pokemon distribution, many johto pokemon not available until late game or kanto
I mean this is really it, but it's enough to bring it down. Ways to fix Johto:
>force linearity by blocking off Mt.Mortar and not allowing you to get the Secret Potion for Jasmine's Ampharos until you beat Chuck. This would allow the level curve to increase. Also add in Drayano's safari zone takeover from SacredGold/StormSilver, as it added a much-needed exp boost that could help the level curve, in addition to expanding TR to actually doing something in what is now "mid-game" and making it seem like more of an actual threat and being an overall really cool experience.
>make more pokemon introduced in gen 2 available in the wild more early and mid-game, and all pokemon introduced in gen 2 available before the elite 4 (or ideally, before claire). add some grass spots near the safari zone so there's actually something to grind on in cianwood, in addition to a new area for more pokemon.
>fix gym leaders to respresent their region, have more diversity, and overall be less of a joke. Why does Chuck have just a Poliwrath and a Primeape? Why not give him Hitmontop and Heracross too? He's the fifth gym leader, he should be able to use four pokemon. Why doesn't Morty have Misdreavous? Or even a Mismagius too. Falkner could add a Murkrow or Natu to his set (and also should drop his Pidgey for Spearow/Farfetch'd, he doesn't need both Pidgey _and_ Pidgeotto). Bugsy could get a Yanma and Pineco.
>make gen 4 evolutions of gen 1/2 pokemon more available. Shiny/Dusk stones are completely unavailable until Kanto, even with Pokeathlon. Pokeathlon making stone evolution pokemon viable before Kanto was excellent, but Togekiss/Mismagius/Honchkrow are screwed over. In addition, Electivire, Rhyperior, and Magmortar's evolution items should be available before Claire. Piloswine should learn Ancient Power by level-up, not just by move relearner.