The trait system oddly enough has good agriculture and good ore be separate traits, but depleted resources as a negative trait gives both poor ore and farmland..

Is there a any reason why you can't have poor agriculture, but good ore or vice versa?  The traits don't cancel out because I still suffer from having a lack of arable land even if the good ore trait negates the secondary ore depletion.

If the traits are as rigid as you imply, i'll suggest two new negative traits:

Empty Mines- Your kingdom has depleted most, if not all the mines in the land.

Famine- Poor Farming practices has made much the land unarable and the current populations of the kingdom unsustainable.