Hey Zied, it is not the best solution but it is the solution advocated by the GAE team. The ultimate solution would be GAE supporting unowned relationships. With regards to unowned and owned relationships, it would be difficult for Roo to work out if a particular reference entity was able to exist outside the parent. I would say that an Embedded class (which is how I believe GAE condenses owned relationships under the covers) could be used for this but GWT 2.1.1 doesn't currently support embedded entities.
The other thing that was created during prototyping was a low level datastore implementation using Twig. This worked really well but fell over due to the currently heavy reliance on JPA in our Finder impl, i.e. we return Query objects instead the results of queries.
In any event the current solution meets a happy balance, given the limitations of JPA on GAE.