Pulses and legumes. I'd really like to see you add pulses and legumes to the game. And fertilization -blood, ash, cow eggs. And a production bonus for exploiting new ground and for crop rotation.
And I'd like to see carpentry have a master-carpentry skill in the skill tree. Medieval carpenters really knew what they were doing, compared to the cheap mass produced lumber production we have today. I mean, they grew trees specifically to get the shapes they wanted, pruning them so they would get lumber at the angles they wanted. And they split lumber rather than sawed it, which makes it much stronger. And when lumber was going to be somewhere damp they put it root end upward so that the moisture would wick out of it....
And what about making the production of grains more complex to get a higher yield? As yet we neither thresh nor winnow, but that could add a whole other layer of possibility. And seed selection, there's another idea.
And what about crops in the turnip family? (Beware of feeding your cows on them as the milk is going to taste... off) Not to mention the crying lack of garlic in the game.