The Hibernate EntityManager documentation states, that:
You may use a combination of all three together, annotations without JPA programming inter
It has been clear: depending on the business and technical needs of your project
But would I have any advantages when using purely Hibernate Core ?
Do not forget both Hibernate Annotations and Hibernate EntityManager is built on top of Hibernate core. So one more layer. Besides That, it rely on its mapping metadata stored in XML files. Some users prefer To use XML files instead of annotations because it leaves the domain objects completely independent of the DAO implementation you choose. But when using annotations, Hibernate with JPA book is clear
reduce your lines of code for mapping metadata, compared to the native XML files, and you may like the better refactoring capabilities of annotations
JDBC >> Hibernate core >> Hibernate Annotations
...
JDBC >> Hibernate core >> Hibernate EntityManager
And JPA 2 fits better what JPA 1 has not been provided. A lot of new features is now available such as
And so on...
Do not forget JPA EntityManager allows you retrieve its underlying vendor-specific provider by using getDelegate method if you need features where JPA does not provide.