Do you have reading recommendations about the science and ecology of farming? Where can a beginner explore these interdependencies you've mentioned?
For vegetable gardening, Eliot Coleman's New Organic Grower is a classic talking about how to design and run a small vegetable operation. He's insatiably curious and he's trying to give you the tools you need to make your own decisions for your own situation rather than giving you a concrete recipe that may quickly become outdated.
Mel Bartholomew's Square Foot Gardening method talks about gardening in small manageable 4x4-foot plots. He had an old PBS TV show, he tells a really good yarn, and he's trying to help people understand how much space plants take up and how much food they produce, and how much time it takes to take care of them, and design a garden that fits into the spaces in their lifestyle.
Nancy Bubel's The New Seed-Starters Handbook is an amazing compilation of specific details about what things affect seed germination and the growth of young plants: temperature, light, timing, etc.
Greg Judy does multi-species grazing on largely rented land: so he talks a bit about the ways they interact and he's also doing it as a regenerative practice so he talks about how he's building soil and improving water retention etc. in the landscapes, and how he interacts with the people he rents from and the surrounding neighbors. Since he's grazing on separated parcels, he's sometimes driving herds down the road from one to the other: his solution to reconciling people to the wait is first to do it early on Sunday morning and secondly to take a cooler and give free steaks to anyone who gets stuck waiting. I own his book Comeback Farms but I think the others are good too.
Simply searching online for specific nutrient deficiencies in crops (nitrogen, potassium, phosphorus, calcium, iron, etc.) can turn up some cool pictures: check out the various US state "cooperative extension" organizations since sharing information about agriculture is pretty much their mandate.
Also ATTRA (Appropriate Technology Transfer for Rural Areas) has a whole bunch of handouts on various specific topics: Vermicomposting: the Basics, say, or High Tunnel Grape Production: An Economic Analysis. They're designed to help farmers make a quick decision about whether something might be for them and where to look for more information, so they tend to be short and clear.
Can you recommend any real-world data sources (e.g. rainfall) that might double as a simulation seed?
The National Weather service has climate data (https://www.weather.gov/wrh/climate, click on the map to choose a region), as does https://www.wunderground.com/
I'd be more likely to browse historical data as inspiration for building structure into games rather than using it directly. How much rainfall do you get yearly? What months does it happen in? Are there patterns to wet and dry spells?
I think it was Joel Salatin (ugh, sorry) who once said that if you can afford it, you should walk your property every day with a notebook for a year before making decisions about permanently siting buildings, farm fields and so on. Get to know the property through a full cycle. It might be fun to do the same thing for your local weather. Maybe a weather club, where you sort of journal simultaneously and then get together weekly or monthly to look back at the patterns?
Do you interact much with other famers, and do you see ways that that could become gameplay?
Some weather patterns are extremely local, like tornados, or (especially in hilly places) thunderstorms/hailstorms, so you could easily have a disaster (minor or major) happen to you or another farmer, and the community could pitch in (wouldn't have to be weather, of course). Maybe they get into a legal brangle with someone in the community, maybe an old-fashioned barn-raising, whatever.
Are you competing with each other directly, or do you occupy different niches. How do you balance that need to make a living against your friendships with other farmers? Are there farmers who come in and abuse that trust and sense of community?
Inter-personal drama in farmer co-ops would also be a really good source of some interesting story material. Everybody trying to find the best way to occupy their niches...
Oh, definitely. Similar to the above, everybody is somewhat competing for the same customer dollars. And just all the usual "running a human organization is actually hard and sooner or later there's going to be drama" stuff.
We had a big split in the farmers' market that we were part of because it was run partly by community members or people who got into selling vegetables to fill a need in the market rather than because they needed the income to survive, and they wanted to just let anyone join. But some of the rest of us were very conscious that this was a limited pool of customer money: even with fairly wealthy tourists, they may have only brought so much cash or have allocated a certain amount to spend, and they want to spread it around and support as many vendors as possible, so more vendors means less income per customer per vendor overall. And...I think there's a National Farmers' Market association, and they have numbers on how much of the surrounding population you can expect to see attending your market, and we were already doing very well in that respect.
There are many things we choose when we model a complex system. We could make a whole game just about buying/selling farm food. We always have to make decisions when we abstract complexity. What are the three to five most important "parts" of farming?
Unfortunately I think this very much depends on what exactly you're making and which aspects you're focusing on. If it's a game just about buying and selling, you might want to look at things like:
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How easy it is to grow certain crops at certain times of year: the prices will drop when something is "in season" and everyone can easily grow it.
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Food fads: can you guess what things are going to be popular and get ahead of that curve?
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Global market: maybe Pakistan flooded the market for organic potatoes and you can't sell yours for love nor money.
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Economic trends: are we in a boom or a recession?
But if you're doing more of a traditional Harvest Moon/Stardew Valley/FarmVille style game with a broad range of products, I'd maybe want to think about:
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How are vegetables different from animals? Vegetables tend to have very low input costs (seeds, fertilizer), but also low sale prices, and then it's all labor. Animals have a lot more up front costs to feed and raise the animal before you get your money back, and higher sale prices, and then the labor per animal is much lower, but over the time spans, there's still not a big profit margin so you still need to keep your time down.
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How does the environment make your life interesting? SimCity style disasters? Ongoing things that build up over time? How much do you simulate and how much can you fake with smoke and mirrors and well-written narrative stuff?
For a small vegetable-growing simulation: I think I'd go with a yearly temperature/day-length curve, and some sort of random precipitation generator that has droughts and floods. And then soil nutrition, I think I'd start with pH that affects the availability of the other nutrients, and then maybe three nutrients for roots, leaves, and flowers/fruit. Nutrients could also be differently available at different temperatures (your tomato seedlings turn purple in the spring because phosphorus is less available in cold soil). They can change availability at different rates in different directions of pH changes. Or some could be water soluble and wash out if there's too much rain. They could also interact with each other: in real life calcium and magnesium and phosphorus tend to compete, so maybe your phosphorus is low because the calcium is forcing it out, so adding more won't help. I think there's PLENTY of room for complexity here.