With the following command the generated settings in persistence.xml are not correct. This might also be the case for other databases and settings, but I didn't test that yet.

 persistence setup --provider HIBERNATE --container JBOSS_AS6 --database MYSQL_INNODB --jndiDataSource java:demo

It sets the datasource to: java:/DefaultDS (should be java:demo)
It sets the hibernate dialect to: org.hibernate.dialect.HSQLDialect (which should be MySQL5InnoDBDialect)