There were RTS games like Earth 2150 which had tunnel systems underground that offers strategic options to ambush enemy base.
An uncharted unknown randomly generated tile based maze filled with monsters is a nice way to open up gameplay options where armies can march underground undetected by enemy forces on ground from A to B. Tunnel entrances should be dotted around the map but may need researches to recover their locations.
In addition, dungeon can offer loots in form of monster drops or treasure chest. Hell you can even design specific 'lost technological' structures of old civilization in a dungeon that offers dramatic game changing advantage such as terraforming the terrain, cause starvation by changing weather system etc.