Why choose one or the other? I would choose a higher-level abstraction that is documented (JPA or JDO) and a low-level API where high-level abstraction does not meet the requirements.
Keep in mind that the API is still not working, so if you choose only a low-level API, be prepared to roll with the changes.
I found that JDO is the easiest way to work, and have not yet resorted to using a low-level API.
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