I think the problem has to do with object oriented programming and classes. Like when you have an Apple that inherits from Fruit, witch later starts looking like a Banana. With prototype you do not have that problem as you copy-paste code instead of couple code. When you rename a variable and have to search more then one function or file, then there are bigger problems with your design, because you are basically using a global variable, even though it's praised as a module. Now does your refactor tool also fix documentation and other peoples code that depends on yours ?

  function Person(name) {
    var person = this;
    person.name = name;
  }
  
  var person = new Person("Jon Doe");
  
  alert("Welcome " + person.name);

  person.name = "Harry Houdini";

  // ES6 example:
  var messages = people.map( person => person.name += " is a rock star" )