This would probably more apply when mastery comes out, but having a higher level (or more mastery) should do something like:

% reduction to pests and pruning required

% increase yield to breeding/harvesting for normal, high-quality, and special seeds/plants

% increase to rare items/mats (stone tail fodder byproducts, magical seeds, hards, sharps, dust, caphras)

% reduction into energy used by workers to maintain farms

I'd rather leave pruning/disease alone. It's where most the experience currently comes from, besides which, there are ways to reduce disease and pests it already.