Crockford's case for prototypal (and against classical) is that classical inheritance is too focused on classifying everything into classes. This forces you to make classification decisions on a problem before you've fully understood it, whereas prototypal inheritance lets you mutate objects as your understanding of the programming problem grows.
Prototypal inheritance feels very alien to programmers steeped in the classical tradition. I speak from personal experience. Crockford's "what you've got is just what you need" really helped me start to accept prototypal inheritance, and recognize the premature classification instinct that had been ingrained in my thinking.