If you ask me:
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Make money be an actual challenge and not just a restock cap. Recettear starts off with the main character having massive debt she has to slowly pay off in a certain number of days, for instance. The threat of bigger and stronger zombies could also be a motivator to save up money. This also ties into what you said about giving the shooting minigame more depth, as currently it feels more like a chore than an actual challenge.
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Shorten days while also making shelves smaller. Outside of the fact they get boring after a while, a shorter day also means you inherently make less money and have to think about what you purchase, why, and how much.
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Make it so there are days where it is more preferable to buy a certain product or a category of products than others. Right now you can just put whatever you want and people will just buy it. By implementing a “preferences” or “random weather” mechanic, you can encourage the player to take more risks and change up their strategy.
Good luck!