hard to do backup/import/export
hard to manage data
every little thing requires deep-diving into GAE-specific details
Recommendations for GAE
I think Google did a pretty good job abstracting Java, but the datastore is not really working for me. Way too much hassle.
My conclusion is that I will use GAE for simple websites with no special requirements on functionality.
For everything else I will probably use Amazon EC2 or similar in the future.