How about little traps your villagers can build (dig) and when an enemy unit walks on it, they fall in. the unit is instantly lost. the pit is only 1x1 tile wide and you can't build 2 adjecent to each other. the pits look just like the normal terrain until someone falls in then. and the villager animation of them diging it out with a shovel. after the pit is used, send your villager to rebuild it, like an expired farm. the pit is uncrossable when its uncovered. but it will fade away after a short time due to erosion and stuff washing it in.
I can't decide if friendly unit should be able to walk across the pit or have to go around, but the ai makes them go around it like it is an obstacle such as a section of wall. pits shouldn't cost very many resources, but should takes a long time to dig out, and a rebuilt pit would take half as long as its mostly already dug.
The enemy ai would act as if it didn't know there is a pit there until someone falls in, then the other troops will treat it as an obstacle and go around. If the enemy player sees the pit construction and it is finished, they can take out pits by attacking the ground with their catapults to destroy the covering and reveal the hole.
Is this a great idea or what?