Good writeup! I think the main change is that App Engine has really morphed into a "You know, you don't have to use Datastore". Cloud SQL was added precisely because of the issues you raise: being on App Engine meant being in a totally foreign world, and not being able to get out easily.
If you were to try again today, you'd take stock Django 1.9 via pip install Django -t lib and using vendoring: https://cloud.google.com/appengine/docs/python/tools/librari... . You point it at your Cloud SQL instance in your DATABASES line (https://cloud.google.com/appengine/docs/python/cloud-sql/dja...) and you're done.
tl;dr: Yep! Things have improved in the last 5 years.
Disclosure: I work on Compute Engine.