With all due respect, it doesn't sound like the simulated violence had much to do with the nostalgia you're describing. Not that I don't believe that violence can't be a tool used to evoke empathy, but effective stories can certainly be devised without hyperrealistic violence.
Some of my strongest gaming memories are of the first (?) level of Rogue Spear (one of the Rainbow Six games), where I was hunting terrorists in the Met. It was fifteen years ago, but I still remember how upset I felt when I saw a virtual character fall down after being shot, and I can still remember the intense despair that crushing my elation when a hostage panicked and ran in between me and the terrorist (and I shot him). I played that level so many times that I can probably still sketch the map. I remember nothing else about the game, but the experience of playing that one map stays with me.
This is a completely different kind of "story" or memory than one's going to get from a game like Borderlands.