Now, I know I'm not the first person to suggest adding compost to the game, but bear with me. With DF 2014 we now have "growths" on plants that more or less serve no purpose: "leaves," and "flowers." My point, is that leaves are an -excellent- stock for fertilizer! Urist McFarmer can rake/gather up fallen leaves and dump them in a compost bin/compost zone. Bin's are more realistic (and can be made of wood/stone/metal/clay) and a proper compost heap does need to be managed (add water/toss clumps around), but this is mostly to speed up the process. Rotten food, vermin corpses, and inedible butcher leavings (nervous tissue, connective tissue) can be mixed in as well. (Urine and feces make fine additions as well, but lets not get into that :S) Ideally bins would be used, and after one is filled up it'll produce compost within a month or two. This compost would ofc serve as a secondary source of fertilizer.
The other half of my suggestion would be part of a farming overhaul. As it stands, there is no such thing as soil degradation. Deep in the bowels of the earth we can mine out a vein of ore in a pit of stone that has never seen the light of day nor any living creature before our dwarves, splash some water on said barren stone, and then reap an infinite harvest of crops without any additional nutrients added. Having to worry about soil depletion as it stands would mean burning vast amounts of wood (that you need for beds, other furniture, as fuel, etc) for the fertilizer to replenish our farmland. However, adding compost made from waste products and worthless leaves would be a much more manageable option. Another option is to be able to mow down dense grass and use that as compost material. This is particular useful for those that live in more barren biomes (tundra, glacier, desert, rocky wasteland, badlands, etc). In these cases, you'll have to bring extra food and a starter batch of compost while you hunt/fish (if able) for food and breach the caverns to grow/harvest cavern moss to add to a compost heap. Crop rotation and leaving farm plots fallow could also help, but fields left fallow would need to be replowed to churn the grass/weeds back into the soil.
These suggestions are twofold- a feasible way to repurpose generally useless items (leaves, flowers, corpses, butcher leavings, grass) and to add a touch of realism into the game. It really does irk me that muddied stone is just as (infinitely) fertile as riverside grasslands. Compost would also be equivalent to fertilizer in game, and would share a charcoal/coke relationship where the two are functionally interchangeable (or compost bins could simply produce fertilizer directly). The bins shouldn't immediately produce compost- like beer and liquor they should realistically have to sit and ferment for some time before use. I am not sure how the game would code it. Part of why I want bins is that could the code be set so that once a bin is full and "set", so many ticks in game code count down before it reopens and produces compost? Proper compost does take management, so the farming skill of a the dwarf that fills it should matter. However, I don't want the dwarf to be tied to the compost heap for a month, and coming back several times in that frame would be troublesome. Could the farmer fill up the bin, prime it to "cook," have his farming skill affect the time/quantity of the compost, then come back a month+ later to open it WITHOUT having to stand there the whole time? Not so sure if the code would allow that.