While I wouldn't normally call this problem a show stopper, for my team it's causing a real problem with our development workflow and we cannot continue without modifying hibernate source.

We use MySQL databases in production and use the schema generation functionality in Hibernate/JPA 2.1 to create our databases. If that was our only schema and data base provider I have work arounds to make it function. However, we are using an in memory HSQL database during Unit testing and because of this defect, all our test cases are failing because the columns are not correctly set to be identity columns. If I was only using HSQL DB I could fix this issue as well.