A little bit of a tangent but just out of curiosity, what would be your preferred option for persistence?
I have loved Dropwizard in the past, which encourages the use of Liquibase. Not right for every project, but it was great when it fit.
For me personally, I'd like to see something like EntityFramework, but in Java. No annotation hell, linq queries are amazing too.
I know a lot of people are moving to just using jOOQ as well.
It's also really difficult to use an EntityManager outside of a JEE/Spring/framework container. They're not thread safe and you have to manage their lifetimes manually.