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The Entity Classes from Database wizard always generates classes with a non-primitive primary key field. This is because the same code is also used for generating CMPs, which require that the primary key field is not a primitive. While non-primitive primary keys work fine for JPA entities as well, this is not a requirement for them and it would probably be better to prefer primitives when possible, or at least provide an option for that. Implementing this requires some changes in the APIs to allow passing information about the generation context to o.n.m.j2ee.persistence.entitygenerator.EntityMember.
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss