Interesting things are happening to GAE these days. They are moving towards custom runtimes using docker that the user can configure...even their datastore API is being replaced by something resembling S3. GAE -> Google Cloud Platform.
Custom runtimes are trying to give people the "No Ops" of App Engine with the flexibility of Compute Engine. Like always, there are tradeoffs, but more options is usually better :)
(I work for Google Cloud Platform)