The biggest problem with the missing APIs is that a lot of 3rd party software and libraries simply won’t work, which means that you loose all the benefits of the mature Java ecosystem. Porting an existing Java application to AppEngine is simply out of question.
Another major problem is persistence. You cannot deploy your favourite DBMS on AppEngine, you have to use Google’s Datastore, which is not a common relational DB. Google makes available JDO and JPA interfaces to access the Datastore. However, these are also partial implementations which provide just a familiar syntax for a substantially different persistence mechanism and create a false sense of familiarity. This is particularly true when you try to refer to the JDO documentation for troubleshooting, but you discover that the semantics of Google’s JDO implementation are quite different. It would have been much better to stick with a proprietary persisntece API and not pretend to fill the gap to reach JDO or JPA semantics.
Another important missing feature are Threads, which makes AppEngine a poor choice for massive computations since paralellization of subtasks is not possible, at least until Google implement the AppEngine Map/Reduce service.
Lastly the overall sense of a finished product is not there. Things that one would expect to work, fail for some obscure reason. Error messages are often cryptic. Apart from an introductionary tutorial, documentation is quite scarce. I guess this is justifiable since AppEngine is still a beta release, but I would rather consider it a pre-alpha. I was expecting much more considerate choices from the smart Google engineers, who have amazed us many times so far.
There were a few things I did like about the app engine. For example, the Eclipse plugin simplifies configuration, testing and deployment. Integration with other Google services are a promissing factor. All in all, Google AppEngine is an interesting toy, but compared to other solutions it’s remains just a toy. If you want to play with it, I suggest you should read this.