NDB is a good hint. But the problem remains that I want PoW to be able to support SQL DBs also. I think SQLAlchemy is a really mature framework for that area. So I need to generate the models in two ways.. I think I need to separate this as an extension since I do not want to have two PoWs, where one is for GAE and one for SQL.

that's the thing with gae, if you want to pretend you aren't going to use it and instead try to abstract away that fact, you are in for a world of pain. you either do gae, or not... no waffling.