The classes get generated, but there are problems in persistence.xml
What problems do you see exactly?
The persistence.xml file is setup during JPA/EJB project creation. Thereafter, the only changes made to this file are the addition of <class> elements to correspond to the tables reverse engineered by you.
We will be adding a special editor for the persistence.xml file in a future release which should make it easier to manage.
Also, is there any way to tell it to not include annotations in the generated files?
No, we do not generate an orm.xml file, so if you do not generate annotations, your POJOs will not be treated as entities which defeats the purpose of reverse engineering. Could tell me what you are trying to achieve here?