Here's a real good reason to prefer Hibernate JPA over legacy Hibernate.
The Hibernate team was one of the most active participants in the creation of JPA.
Effectively, then, it was how they would have designed Hibernate with the resources and knowledge that they gained from their previous architecture.
The fact that you can (and I have done so) switch between JPA providers (from Apache OpenJPA to Hibernate JPA) with just 3 changes to a project's
Maven POM and the addition of 2 simple config files is nice, too.