You are correct that you can't use java methods for identification, nor should you anyway.
And you said it yourself, the default mapping is insufficient, it always will be. You will need to go in manually adjust properties for identification to something unique and static for your objects.
That being said, it absolutely can be done. My team has over 2000 tests automated for a Java point of sale.
I recommend reading everything here: http://support.smartbear.com/testcomplete/docs/testing-with/object-identification/index.html
I should have been more clear about our use case: we don't want to write tests, we were hoping we could capture real user sessions from a production environment and replay them in a cloned environment.
While we were expecting that it would not fully work out of the box, we were willing to spend some effort to make it work, but for this use case what matters is flexible mappings, not flexible scripts
