I think technology could be a better answer than resources. Just create a couple of purely dead-end military techs for each era which give bonuses to particular units. A "Tower Shield" research (reqs archery/bw) for the ancient period allows units to get cover for any melee unit built in a town with a barracks, for example while "plate armor" (reqs MC) could be similar for shock during the classical period. Making these complete dead ends would also decrease the disadvantage of isolation. (an isolated civ wouldn't need these promos)