(...) what, pray tell, is the point of protocols, other than backward compatibility with historical fragile ducks (at the cost of future backwards compatibility)?

Got both of those wrong. The point of protocols is to have a way to validate duck typing errors by adding a single definition of a duck. This is not something that only applies to backwards compatible, nor does it affects backwards compatibility.

Why are people afraid of using real base classes?

You're missing the whole point of prototypes. The point of a prototype is that you want duck typing, not inheritance. Those are entirely different things, and with prototypes you only need to specify a single prototype and use it in a function definition, and it automatically validates each and any object passed to it without having to touch it's definition or add a base class.