In case you missed it, the latest AppEngine for Java release adds support for JAXB (the single most requested feature according to Google’s announcement!). In addition, AppEngine 1.2.8 significantly beefs up ORM support, now supporting inheritance, IN queries, and much more.
I had already found workarounds to these limitations for my current project, but the latest release further demonstrates Google’s commitment to a superior platform and eliminates many more excuses for not giving it a try.