Some things that came to my mind:
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A more diverse wildlife. Even in New England there should be more than 5 different types of animals.
(Btw: Why are we sticking to this whole New England thing again? The average player probably doesn’t even notice the scarce hints, and getting rid of New England would allow for different biomes, a vast increase of wildlife, etc.
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More and different plants. Having just two different kinds of flowers is kind of sad.
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A system that allows for re-randomization of items every time you play. (Is this implemented already?) Just the way e.g. Scrolls and Potions are handled in every other roguelike. This could go hand in hand with an extended flora, mutagens, mushrooms and possibly even books.
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Houses (and regions in towns) of different levels of wealth. Perhaps 5 different levels for regular houses (plus Mansions), big and expensive houses should be a lot harder to get in than your average slum-shack, yet also allow for looting of precious advanced items.
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Ability to include Mutations in Professions (already possible?)
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I also second wind and puddles. Both seem very realistic and cool, although certainly a big chuck of code.
EDIT: 7. Make spider-eggs craftable into something that’s not (as much) disgusting as the basic egg. I jjust raided a black-widow-house and have twenty of those good, nutritious eggs which I can’t eat without getting my character to be depressed. THis might be possible, but my cooking of 4 was not sufficient, then.
EDIT2: 8. (This one should be easy, but important) Group the construction options. One category could be “Furniture”, one could be “Fortifying”, everything that doesn’t really fit in a category could be “Other”. I guess a makeshift version of this could be done by adding “fake” recipes which serve as separation lines.
Tell me which of those are possible to add by myself and I will gladly do so. Preferably in json format, I do know some C++, though, if that helps.