I'd have to agree that Django on appengine is a big pita for the reasons you mentioned. Django is a large framework, and was simply not designed with interchangeable backends in mind. Getting it to work either requires a lot of black magic monkey-patching or foregoing the majority of built in features.

On the other hand, I have found the datastore api (and most of the other apis) to be well designed. It works very well with lighter frameworks such as tornado.