I think a feature that would come in handy would be one where you can set nicknames for the NPCs, like you do for the player's character during character creation (e.g.: my protagonist is called Edward and his nickname is "Eddie"). After a while it starts getting difficult to keep track of who is who just by name alone.
There are some characters with roles that give them nicknames ("The Best Friend", "The Porn Addict", "The Arcade Denizen", etc.), but these are only one or two dozen of these while there can be up to hundreds of nicknameless characters.
A nickname feature would come in handy specially for people who like customizing the characters (such as myself). It wouldn't need to come up in conversations with them, it'd just need to appear in the "People" tab.