Robert and everyone: we hear you. Please keep in mind that App Engine Flexible is still in beta, and the Python compat runtime itself is in alpha. We're still doing a lot of work on both and we're still collecting user feedback. Things like this mailing list and the public issue track are some of the ways we collect feedback, so while it may appear dismissive for us to say "file an issue" - we do take those seriously.
Regarding endpoints itself: I can't speak any definite plans, but I can stay that we are investing in endpoints and that you should stay tuned.
In the meantime, I would recommend looking into "hybrid" applications - use app engine services (neé modules) to have one service running on standard that works as your API frontend, and another service running on flexible that can handle the heavy lifting.