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limit free healing. we don't need a pokemon center in every town, and it would make the towns with one feel special. Instead, make ethers available from shops and encourage the player to plant leppa berries. This simple change will have cascading effects on the rest of the game, such as making money matter more, encouraging more natural backtracking for berries and healing, and enables players who know what they are doing to start optimizing their gameplay in ways the current design lacks.
Battles themselves will never be all that hard on their own, so we need to test the endurance of the players instead.