Plant Hybridization
I believe hybridization of plants should be included in the game, not only with it open up opportunities for new cooking recipes, but a whole world to explore that would give the player some sort of randomness associated with plants.
I think more furniture options would also be a great addition to the game.
Things like tables, more types of chairs (like chairs with plush bottoms that you use linen/silk and wool to stuff, or maybe even the implementation of the cotton plant!), screens (like modesty screens, more carpet options (maybe even wood tiles), or carpets you dye with blueberries or poppy flowers).
The options are endless.
Hybridization would work in a way similar to an herbalist table and chicken coop, but instead a "work station" that would house plants and seeds.
Plants would grow and interact in an environment where there is a chance that a random seed would be produced, one of either Parent No. 1, Parent No. 2, or a combination of both parents.
Here is a tree of what the hybridization would look like.

Of course it would continue on on even further getting to more complicated hybrids, but it will reach a limit, meaning you can't have 3 different plants in one, like a Poppy, Grape, and Flax hybrid, instead a limit of 2 plants being expressed in the hybrid. But that product would carry "genes" of the parent, thus making it possible to produce a "baby seed" that shares no resemblance to the parents, but earlier on in the "gene tree" an ancestor could be like that "baby seed". (i.e. Hybrid Poppy and Flax mates with Hybrid Grape and Flax, and produces a pumpkin "baby seed" that is earlier on in the gene tree). Of course the chance of a pumpkin coming from a Hybrid Poppy and Flax and Hybrid Grape and Flax would be slimmer than producing a Poppy "baby seed". It would get quite complicated in the end, but It would be interesting to breed certain seeds.
The number of possibilites would be ... hmm... I believe (different species of plants) x (different species of plants) = 100ish?
Tree Hybridization
I believe this would be the first thing to implement a Hybridization feature into. There are fewer trees than crops, and trees would be good guinea pigs for a potential hybridization feature to the game.