So far, I always prefered to use Hibernate directly rather than JPA 1.0, because JPA was lacking some of the important features I needed and Hibernate provided: Criteria API
On the EclipseLink Project we have been focusing on a strategy where users can stick to JPA as much as possible and we have been working to make our many advanced features easily available through extensions so that you can minimize your use of our native API. Obviously as the JPA reference implementation we need to be compliant but JPA offers several extension points that we make use of including query hints and persistence unit properties. Some features are enabled through EclipseLink JPA specific annotations and/or eclipselink-orm.xml as well as API but as noted with JPA 2.0 many of these can be handled by the standard configurations.
Ultimately the benefit is that by staying with the standard as much as possible you can leverage a common knowledge base as well as tooling and integrations. Advanced ORM capabilities are also very important but should only be needed in advanced cases and the usage should be well isolated with minimal coupling.
Doug