EJB 3 Entities is now called JPA, JPA is just a specification. So the question then lies in which implementation of that specification are you going to use. Hibernate implements JPA, so does TopLink.
In the cases of those two products, they are also more than just JPA. Meaning they also have a lot more implementation that goes beyond the specification. The JPA spec does not cover every single scenario you might come across, which requires you to use the products specific stuff.
Hope that helps clear things up. It is not an either or question.