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Here's an idea I had to hopefully give the games' dungeons a chance to be more complicated and puzzle-oriented.
Early on, the game gives you the Squeaky Hammer item. This item has two effects. First, it can be hard mapped to a button via register and repeatedly used in the overworld. In this way, it can be used to quickly hit switches that toggle puzzle elements. If you wanted ranged switches, the Squeaky Hammer button can be held and released to throw the hammer instead of swinging it, with the item returning to you almost immediately.
The item's second effect is that it seriously annoys wild Pokemon and drives them away from the trainer for about fifteen seconds. This ensures that as the player is heavily involved in trying to solve a dungeon puzzle that they are also not harassed by random wild encounters. This means the Hammer can also function as an emergency repel item, though those would still exist for their ease of use and for their lack of a squeaky sound effect each time they are used.
You would obtain the Squeaky Hammer as a reward for using it to drive Diglett and Dugtrio out of a farm field in a Whack-a-Mole minigame.
