There are a number of odd things with improvement yields, they really need a full pass.
I would suggest:
Farm: +1 food, +1 food with freshwater from civil service, +1 food from non-freshwater from fertilizer.
Mine: +1 production, +1 production with freshwater with metal casting, +1 production from non-freshwater with dynamite.
Lumbermill: +1 production, +1 production with freshwater with machinery, +1 production from non-freshwater with steam power.
Village: +1 gold, +1 gold with freshwater with optics, +1 gold with nonfreshwater with economics.
Pasture: +1 food, +1 food with freshwater with civil service, +1 food with nonfreshwater with fertilizer.
Plantation: +1 gold, +1 gold with freshwater with guilds, +1 gold with nonfreshwater with fertilizer.
Camp: +1 gold, +1 gold with freshwater with compass (?), +1 gold with nonfreshwater with steam power
Academy: +4 science, +2 science with philosophy, +2 science with education, +2 science with scientific theory, +2 science with atomic theory.
Customhouse: +4 gold, +2 gold with mathematics (or currency), +2 gold with guilds, +2 gold with or economics, +2 gold with electronics.
Manufactory: +4 production, +2 production with iron working, +2 production with machinery, +2 production with industrialization (or steam power), +2 production with replaceable parts (or combustion).
I know there is a problem with how many yield increases can be displayed on a tech in the tree tree, but I think not displaying the bonus on that screen is a smaller problem than not having the bonuses well spread.
It doesn't make sense having much larger yield increases for some improvements than others.