Well, in that case, have various crops influence the levels of each nutrient according to the raws. Maybe Plump Helmets use up everything, and pig tails fix nitrogen. Maybe you can grow blade weed to increase the phosphorus levels, and so on.
And, of course, leaving the fields fallow should increase everything slightly.
Yes, that is entirely the idea behind the Crop Rotation system - different crops take up (or even replinish) different amounts of nutrients. In real life, letting a field "fallow" is not a matter of simply not planting anything and hoping that nutrients come back, you plant crops that will replinish the nitrogen in the soil through Nitrogen fixation, and burn them or plow them into the soil so that all the nutrients they collect will become part of the soil for the next round of serious crops.
(That is, letting a field "fallow" does not mean nothing is growing, and the soil magically gets nutrients back, you have to specifically plant something that will add nutrients back into the soil with the specific purpose of not harvesting anything useful, but instead just killing the plant, and using it to fertilize the soil for the next crop.)
Grains like wheat and corn can feed so many people for the smallest possible acreage specifically because they consume such massive amounts of nutrients like Nitrogen, and convert it into easily digestable sugars and protiens.
Less attractive crops, such as legumes (I guess that would be the prickle berry of this game...), which replinish Nitrogen, are then encouraged to be grown simply because of its ability to help sustain the growth of other staple crops. This was, in fact, part of the importance of George Washington Carver (who is so much more than a guy who made peanut butter) - He saw that southern farmers were depleting their soil, and knew that peanuts would replinish the soil, and so started creating products based upon peanuts (shoe polish, paint, ceramics, etc.) so that there would be a greater demand for peanuts, and they would become a more attractive crop to plant. (This is also essentially the roots of modern bioengineering.)
So, what we get is three ratings of fertility that are all used up and refilled by various different crops, and it requires quite a lot (very FUN) of experimenting to determine. It's moddable, potentially expandable, and I even feel it's clear to a reasonably astute newbie that if the such-and-such levels are going down in the farm, it might be bad.
Honestly, I would expect any working system to almost instantly be put up on the wiki, along with "Let's Play" or tutorial versions of how to make easy sustainable crop rotation systems for the noobs, so that they can pretty much just paint by numbers for vanilla crops.
The three farming factors are actually rather arbitratry- they could be Nutrients, Minerals, and Acid, which could clearly be conveyed in a way that fits the theme, like "The soil is too acidic for this plant" or "The soil is rich in nutrients".
That would serve to make the mechanics more approachable.
Well, minerals are nutrients.
If we are speaking of adding or subtracting arbitrary numbers of nutrients, we can always add the next layer of (less heavily used) nutrients, secondary macronutrients (as opposed to the heavily depleted "macronutrients", NPK), which are Calcium, Sulfur, and Magnesium, and below that, the micronutrients , which are Boron, Manganese, Chlorine, Iron, Zinc, Copper, Selenium, and Molybdenum... which are so rare most modern people don't really know what they are.
I still think this would be fine:
"Plant leaves look healthy"/"Plant leaves are slightly pale"/"Plant leaves are showing slight yellowing and somewhat small"/"Plant leaves are yellowing, new leaves are progressively smaller, and show ruddy undersides"/"Plants are stunted in their growth, and are discolored yellow and red"
If they are always displayed in the same order, even total Noobs would understand there is a gradient from good to bad going on, and "look healthy" means they don't have to worry.
If things start to get bad, then, like with designating a farm telling you that you need mud in yellow, the game can say what kind of fertilizers can potentially solve the problem. (If there is acutally too little space on-screen for this, there might actually just be a button you could press for "farmer's advice" that will list all potential fertilizers, sorted by usefulness in that situation, including all crops in the raws, including modded ones, that replinish that form of nutrient.)
Of course, this also means modding will enable uttelry breaking the system by simply making all crops not take up any nutrients at all if you REALLY want to ignore the whole system. (Which might be the ultimate noob's way out...)