From what understand GAE and MongoDB are similar and I have not used GAE enough to act like I know everything in the universe however GAE does use strings to build queries and even though they seem to implement a PDO type accessor to their querying it does still beg the question of whether that creates security issues.
Also I must admit looking over the examples here:
https://developers.google.com/appengine/docs/python/datastore/queries
It seems as though the GAE requires quite a bit of work in each file to get it to work properly, much more coding than I do for Mongo.
I have also noticed that sorting and filtering requires that properties exist which technically means its not totally schemaless since you can't perform any query on any set of documents.
My final conclusion is that it depends on the app, you gotta question what type of queries you are gonna do (are you gonna make good use of MongoDB's subdocument structure for example?). I personally would also benchmark the two on your hardware to see which runs faster and scales better for your particular scenario.