Sorry but I'm skipping pages 2-15 here, and pretty much responding to the original post, and to silverionmox.
I have a problem with "realism" being the (only) goal in making anything... The objective should be to make something entertaining and engaging. Simply making farms larger, and require a larger portion of your workforce doesn't make it more engaging. Making a player sit and measure Ph levels in an obtuse UI, and try to force dwarves to use one specific kind of fertilizer as opposed to several dozen others is also a problem. In fact, considering how often people just flat-out ignore work cancellation orders, it could be lethal to require too much micromanagement.
I think it best to work from the ending backwards - what level of involvement we players want in our farms, and then figure out what system would give that to us.
One of the complaints is that it just plain takes too little effort to set up a working farm - which is entirely valid. A 5x5 plot can be set up within a minute of starting a new fort, and a single farmer can get your entire food supply nailed down for the first two years. Making something like 20% of your fort farmers just to hit subsistance levels, however, is absurd, especially since that doesn't even leave room for farming to craft textiles. (And my current fort has about 300 tiles farming, most of which are to dyes and cloth plants, since I have a very large textile mill (five each of the various textile workshops) as my primary income source... Call me a tradesdwarf.)
Basically, I don't think "throw more dwarves at the problem" is a good solution. It just means you have more dwarves being tied up running longer laps hauling food than you do now, and it doesn't really involve anything more from the player, but giving him less dwarves to do other things that the player considers more important and engaging, like defense construction.
Something that I do think should be a goal, however, is some kind of "conservation of matter". Farms right now produce food from nothing (a "fountain"), and the food dissapears into nothing when eaten (a "sink"). It's not exactly right, but at least it balances out in a way. Metals and stones, on the other hand, are basically sinks without a fountain, unless you use obsidian farming, and excepting traders. If we are to start using stones as fertilizer (not a bad idea to begin with), then we are going to be needing to mine stones at a certain pace just to be put into a process that ends in a sink.
Granted, I doubt many people ever hit a point where they've completely mined out their entire fortress site, but a goal of "realism" shouldn't produce a model that annihalates matter.
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There are two things that I think would produce a good system... First, I agree with a system of requiring farmers to supply water to the farms. Simply making them dump water with buckets may be silly-seeming, but probably better. We don't want players setting alarm clocks for themselves just to remember to re-irrigate the fields with controlled floods, it's far too much micromanagement. It would be best if we could trust dwarves to be able to irrigate their own fields, but let's face it, they're not smart enough to know to engrave the inside of a room instead of running outside when going outside is forbidden, straight into a seige, unless you actually lock them in the room until their work is done (and remember to let them back out). In short, not holding their hands through a flooding is like making an engraved invitation for a watery doom. Better, simply having a water source near the farm should be fairly fast and easy to track (especially if a well), and use something we are already fairly used to.
Also, above-ground plots should benefit from rain... walled-in above-ground farms should be potentially as easy to manage as things are now... after all, real-life wheat farmers really did pretty much only work during planting and harvest times, and did largely nothing during the Winter.
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The other idea is a simpler version of soil quality. I think the best way to handle soil quality is to use a very simple metric - instead of having actual mineral levels in the soil, it would be best to keep this down to a metric of something like "red dirt", "brown dirt", and "yellow dirt", representing some general soil quality, without getting into chemistry. After all, these are just middle-age-tech dwarves, soil color is basically the best indicator they have.
The way that this would require player intervention should be entirely front-loaded, so that there is no micromanagement once the ball gets rolling, unless you want to change crop loads.
Each plant could have soil/nutrient requirements (depleting one color heavily, and a different one lightly), and potentially replinish one color of soil at a certain rate, as well. There should also be some kind of "fallow plant" (like clover) that would help greatly replinish the soil, while at the same time being generally useless, except as animal feed. Clover "plowed back in" by not being harvested would boost soil even more. The idea should be to allow for a crop rotation schedule that would give a carefully scheduled farm better production rates than one simply set to "farm plump helmets forever", especially as soil depletion would give less and less return (although not to the point where farming would be useless... hopefully, this shouldn't be a punishment for anyone who doesn't want to read up on the system, but a bonus for those who do take steps to maximize their gains, while even a poorly-designed farm can produce enough food, if it were simply large enough, and well-staffed enough).
To help in this, it might actually be better to create a "farming screen" somehwere in the interface (like from the z-status menu, where each farm plot can be scheduled individually, both for crops, and for fertilization), so that you can plan crops on a loop multiple years in advance, rather than the current, rather user-unfriendly system.
Fertilizer would still be useful, of course, but would need to be broken down into what "color" of soil they produced. It would actually probably be best if "chunks" and "remains" decayed into an invisible, but collectable "soil" item. These might produce, say, brown soil, while potash produced, say, yellow soil. (I have no idea, really, what soil color really denotes, I'm just throwing out arbitrary examples.) Since dwarves live in a world where the only excretion is vomit and blood, and I doubt we really want vomitoriums just for fertilization purposes, chunks are the best source of additional fertilizer from renewable animal sources. Fertilization in this way could let you keep running one specific crop you really like/profit from more often.
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As a side effect of this sort of system, it should actually be possible to have a much better selection of crops in the game, and not just in terms of making more dyes. Using dyes as an example, however, hide root is much maligned for its lack of value when dyes are useful only for adding value. If hide root were to replenish more soil than it depleted, a low-value produce would still be viable. Meanwhile, sunberries or other high-value crops might deplete heavily, requiring much fertilization support to make viable.
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On a completely seperate note, I do think it would also be useful if all crops didn't die on a new year (for whatever reason they do this), so that there could be a potential for "orchard" farming. Especially in warmer (non-freezing, that is) climates, having fruit trees that only require very occasional fertilizing and watering, but which take a year or so to raise would produce an interesting variety in the types of crops that one can produce.
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I would also like to suggest (although this may be more suited to a seperate topic) making a "garden" - basically, useless flower crops or shrubberies or the like that simply raise room values when they aren't picked (or make flower vase furniture or decorations for other items if they are), or can be used to create a "plant garden" to go along with a statue garden. It would especially give those darn elves something to do with their time, and it's partially inspired by my own dwarven civ's elf queen (whose only job beforehand was "farmer").