Things on bones and salinity
Ground bones is already pencilled in as the "primary phosphorous source", especially since most other rotting matter is decent in Nitrogen and Potassium, but not Phosphorous. I'm not sure that people would actually perform long-distance trading of ground bones, though, maybe just regular bones, since they are more versitile materials, and can be used in bone crafts if un-ground.
As for salinity in the diet, yes, I was thinking of that, as well, and may do a full bit on nutrition, since talking about nutrition was a way to make farming more interesting, as well. (Salty diet means salty urine, which means salty fields if you apply urine directly to the fields as a fertilizer?)
One of the problems, especially when I start talking about animals and the need to feed them, is that we're going to need to start making animals eat different amounts based upon their masses (and potentially metabolisms). Elephants and hoary marmots would currently eat the same quantity of food if we don't make creatures start needing to eat more than one unit of food per meal. Part of my suggestion was that we just start multiplying the amount of food dwarves eat up to some arbitrary number like 6 (because of their size), and that way, a single tile of farm's harvest of 1 to 5 units of food, which makes farmer skill have unrealistically huge impacts upon food production, and we can move towards something where a farm tile of 3x3 might produce between 15 and 30 units of food per harvest, which would feed 2.5 to 5 dwarves with 9 times as much land.
Nutritional requirements might also do interesting things to help encourage farming diversity, as well, although it may not be as necessary, eventually. I'm already doing plenty to encourage diversity in what crops you plant, from crop rotations and pests.
RE: watering crops & irrigation
Really starting to suck you into it, now, isn't it?
I was thinking of a drainage value, although it was more to repesent the needs of different plants, since my research on different crops from around the world frequently mentioned the need for such-and-such a drainage. Relating drainage to water loss would be another good, if somewhat complex, method of intigrating it into the whole.
As for how much water soil can hold, well...
different soils will hold different amounts of water in real life, and it's based upon the amount of biomass in the soil, although making the maximum size of one variable dependent upon another variable is just too freaky a system even for DF. For now, let's just say that something like how many units of soil nutrient water that 1/7 map water will translate into is a "calibration" problem, one that can be determined after we have had a chance to look at how the whole system operates, and can fine-tune to something that makes the whole thing operate sensibly, since it's just a single variable that can be easily altered to suit the needs of making things "look right". There's also no problem with having 1/7 map water make up 127 nutrient water or 100 map water or anything else.
I'm not sure having three entirely separate variables for measuring the direction water seeps is justified, however, as I'm not sure how we could properly model upward or downward seepage all that well, unless we're going to have something specifically about refilling aquifers by having seepage or something like capilary action forcing groundwater to the surface. (Unless by "upwards drainage" you mean evaporation?)
Having water filter downwards and create or refil aquifers and caverns through that method might be interesting, although I would have to spend some serious time thinking through the exact mechanics of making that work properly. At first, I was having trouble thinking of ways in which the player could interact with such a mechanic so that it would make any difference if we were using it as opposed to just abstracting aquifers refilling automatically, but if dwarves pave over enough open soil that allows water to permeate and refill the aquifer, you could potentially start causing even more overdrafting problems. Such a thing is possible, but aquifers are generally large enough that I'm not sure fortress mode would have the capability to significantly impact that the way that you can make the patch of land you can actually reach turn into a desert.