Chores don't feel like chores when they're this fun.
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I don't think it's necessary to turn everything into a minigame, I think it's already an improvement if you can see the process happening in the world.
Say for example that you have a structure that turns one resource into another. The simplest way to implement this is to open a menu when you interact with the structure, put the resources in and then take the resulting resources out (after the process is done). However, this makes the structure just a front for a menu.
An upgrade is if the structure plays an animation showing the input resource being turned into the output resource. It at least makes it feel like the menu is an interface for the structure instead of the structure being a front for a menu.
It's (often) even better if there's no menu at all, or at least not one beyond configuring the structure. The main way to interact with the structure is to do so physically. Which can include a mini-game, but then you have to make sure the mini-game doesn't become annoying, which can be a tricky balance.
One important thing is that the presentation of the game affects the expectations of the player as well. Opening a menu when a player interacts with a flower pot breaks immersion more than opening a menu when a player interacts with a sci-fi hydroponics pod.
And mentioning player expectations, I think this article was interesting as well:
Dwarves embody the universal human urge to wade into a flooded tunnel in search of dinner.
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Based on the presentation of the game, what could be considered a bug can, in fact, be considered a feature.