I like the current system of farmland nutrient level and how it strongly encourages crop rotation, but it could be better. Currently, every crop reduces a nutrient level, but none of them improve any. For example, soybeans have been known to improve nitrogen levels in soil. To be balanced in VS, I'd say it could improve the soil a few percent, likely no more than 5%.
Cover crops, such as clover, are sown strictly to be tilled back into the soil. Clover can survive most winters and vastly improves the nitrogen levels of the soil, but I'd say it should be no more than 15-20% improvement in VS. Clover is also a favorite food for rabbits, so you might still be able to attract/trap them throughout the winter.
I do not think ALL crops should improve something, but certainly at least a few, and maybe not by much. That's what cover crops would be for. Unfortunately, a lot of cover crops are used to prevent weeds and pests, so they would not directly translate into the game.
"main" crops that may replenish other nutrients: radishes, rye, peas, soybeans
potential cover crops: alfalfa, buckwheat, mustard, vetch, clover, oilseed