That is a really good point I haven't thought about that much, and is probably a decent reason for my distaste of FC3. In Call of Pripyat, I can tell you of a bunch of locations, even if I can't remember their names. That power plant with the electricity anomalies and poltergeists, that factory where the mercenaries are hooked up with intel, that bridge near the giant psychic rift, and basically any location that has anomalies or people. In Fallout, you have all the major towns, like Megaton, New Vegas, Rivet City, Vault City, Goodsprings, Nellis, Necropropolis, and Reno. In pretty much any of my favorite games, I can rattle off a list of locations that had a unique feel or story to them. Even in Far Cry 2, which had major gameplay issues, I can remember a bunch of locations set up that have no actual name. You have that one platform on a hill that provides a good overlook of two checkpoints and a safehouse, along with any approaches, perfect for sniping, you have that one villa protected by a series of guard outpost in the jungle, that group of guardhouses set up alongside a bay, that one group of buildings on the second map located in the middle of a set of mountains and hills, with one that provides a perfect view for sniping and mortar attacks.
Far Cry 3... had that one hill where a starting tutorial took place, that gorge filled with bodies that the insane guy kicked you down, and those caves where the boat is holed up.