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I think the only way to introduce real difficulty to Pokémon main story would be the option to make the game play with Battle Tower rules.
>All levels set to 50 for Trainer battles
>No items allowed in battle except for held items (replenish if they're used) and battle items like X Attack/Defense/Speed
>Heal after each battle because you'd be screwed otherwise
>In wild battles and the overworld, your level functions as it actually is and gaining EVs and evolving will reflect in your Trainer battle stats
>You can still gain experience and EVs from Trainers, but it's based on the actual level of their Pokémon rather than the level 50
>You can use up to the same number of Pokémon as your opponent, and you can pick which Pokémon you want to battle based on the preview of the first Pokémon in the Trainer's party
>The further you progress, the more Pokémon that Trainers will have, and the more likely it is that their Pokémon have held items, high IVs, are EV trained, and have more strategic movesets
I'm just not sure how healing items should be implemented if you recover after every battle. Maybe if you don't recover after wild battles, but your current Trainer battle stats ignore your current wild battle HP. Or maybe they should be allowed and players for have to heal manually after Trainer battles. It would certainly give those items a purpose and make them far more integral to the game.
Also wondering how Legendary Pokémon should work. Most should be optional and up to the player to track down and thus function well as rewards, but I think it would be a shame if they broke the game's difficulty just because you found them. Maybe make it so you have to raise them enough (EVs, friendship, teach them the right moves) for them to be viable, but make it worth the player's time.
Anyway, this would be a difficulty OPTION, like a Veteran Mode.