I found the same problem and came to a conclusion that it is very
difficult to achieve 100% source code compatibility between GAE/JPA
and non-GAE/JPA solution. So I ended up with two sets of entity beans
and two set of queries (behind the facade). Also the transaction model
in GAE is different. So I achieved something about 10-15% code
different and 85% -90% code the same. I'm not very happy with that but
that way I avoided the "Lowest common denominator" phenomena. By using
TO (Transient Objects) I have the client side (GWT) exactly the same
for this two models.
So after a lot of refactoring I migrated to GAE keeping backward
compatibility and I'm able to work on GAE/JPA and non-GAE/JPA at the
same time.
But it is my experience, may be someone else achieved a better
performance, I'm looking forward to hear about that.

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