I was aware of most of the limitations of AppEngine that the author of the article mentions after just a few hours of experimenting with AppEngine. Now, AppEngine now no longer gives me many problems.
I think the lesson is to do a lot of experiments before committing to technologies.
I don't use the Python SDK. Most of what I have done has been using Java (but with small Clojure and JRuby experiments). One thing that helped was to start using Objectify instead of JDO (as an example).
At this point, I think using JDO on App Engine only makes sense if you're porting an existing JDO application to App Engine.
If you're starting from scratch, Objectify is the way to go.