In short those "negatives" are actually perfectly reasonable when you consider what GAE was designed to be: A Google managed PaaS that handles all the hard parts for you IFF you follow the platforms conventions. The problem is that others see it as a drop-in for EC2 and get burned as they throw away their previous tool chains like Postgres, Redis, and the entire networking stack.
[1]: http://stackoverflow.com/questions/4114902/how-can-i-run-a-w...
I don't recall whether Ingress specifically ran into anti-patterns (or we advised them early enough to avoid them). As I left Google in 2013 I am not sure what the experience of Niantic was with regards to Pokemon Go.
Before App Engine used snowflake IDs for the App Engine datastore IDs were allocated sequentially. The App Engine datastore is based on Megastore [1] which is based on BigTable [2].
If you read massive amounts of sequential keys you could potentially run into issues with the automatic management of tablets. Compaction/splits could introduce terrible performance.
Since Niantic Labs operated within Google there was more flexibility around budget, but with other customers (for example Snapchat), you also needed to carefully control your cost. Perform projection queries (always a good idea) to only return the data you absolutely need and many other optimizations. There is a lot to learn that is specific to App Engine, for example [3] (this is a very old and now outdated SO answer I gave).
From my perspective, designing a high performance and scale, cost-effective application on App Engine is very difficult, but not impossible. This is of course only the case if your application is a standard web application (or REST API). A lot of functionality you may want (support for certain system libraries or connection protocols) may be unavailable.
IMHO, Google Container Engine (and similar services) eliminates many of the use cases for which I previously would have chosen a PaaS such as App Engine. I am in full control of my runtime and application environment without the need to learn proprietary APIs or system behavior, while not having to worry about managing the server infrastructure.
[1]: http://research.google.com/pubs/pub36971.html [2]: http://research.google.com/archive/bigtable.html [3]: http://stackoverflow.com/questions/14698119/httpexception-de...
That being said, they really should've done better at predicting hype, especially since they had beta sign up and all.