The main reason I've come to avoid prototypes in many cases (except when I really need to control memory) is that you can't keep any kind of information private (via closure) and share it across instance methods. It has to be a property on the instance, and is therefore accessible to anybody with access to the instance.

Conventions (like prefixing with _) are great, but they can only help loosely enforce encapsulation and provide no form of real privacy.