I'd also like to say (in its own seperate post) that I've been thinking about outright procedural crops. The basic idea comes from trying to solve the "problem" people have with certain sets of crops becoming a "permanent solution" to how to set up growth cycles - if every fortress's crops are different, you have to figure out what works best with what every time.
We would still need the ability to mod in our own crops, but we could have crops that change based upon a formula that keeps their difficulty in growing them balanced with their products.
Even better, this would allow us to have unnaturally selected crops through worldgen-era domestication of crops, as had been suggested in the FoTF thread (sorry, I couldn't find the specific post in a search, or remember who said it). This means that dwarves would have procedurally generated improved versions of underground crops, while elves and humans could have improved crops exclusive to their own culture, that will not grow wild (although perhaps you will find the wild versions of their crops).
For an idea of what unnatural selection can do, consider corn. Corn was originally just a grass, much like wheat. It was selectively bred for more kernels - from a dozen or so to hundreds on a stalk. It was bred for larger, more sugary, and more juicy kernels - to go from wheat-like seeds to something that is filled with moisture. In the 18th century, it was even explicitly bred to produce certain types of oils, fats, or sugars (Partially hydrogenated corn oil comes from corn that is specifically bred to just have glucose and sucrose in its kernels) that could be used in chemistry. Even things like popcorn aren't dehydrated corn kernels, they're specially bred to have hard shells that trap the moisture in so they will explode when heated.
These improved crops could produce much more food per acre, but have potentially drawbacks. The soil nutrient costs could be bumped up somewhat, especially as they become more extravagantly redesigned. The major factor, however, should be in a greater prevalence of pests that target that specific type of crop.
The more people worldwide growing that staple crop, the more a pest specialized in feeding off it will flourish. Such crops may have more pests, or more pervasive pests. The pests, of course, should be just as procedural as the crops themselves.
With luck, the ways to combat pests could be just as complex as the rest of the system - growing specifically bred funguses to combat specific pests or diseases, or even just using certain types of birds or introducing certain insects that will hunt down insect pests. I've also previously lightly mentioned that some kinds of plants are capable of repelling types of pests. Planting flower beds alongside vulnerable crops whose flowers repel the specific types of pests that will hunt some of your favorite crops will allow you to grow them in peace, at least as long as you don't get too excessive in your growing of the crop.
As I've said before, I really think pests are the best way to introduce a really scaling set of complexity as your fortress's agriculture becomes larger (Although sheer size and infrastructure for the water requirements will also contribute. Don't forget, either, that fertilizer and liming agents are not necessarily found in infinite quantities.)