Although I do like Cloud Run (and Functions, to a lesser extent), App Engine has (had?) some useful features that are not present on those offerings. What I miss the most is the async worker/background jobs feature. Cloud Run/Functions forces you to use HTTP requests for everything (Functions has some exemptions for a handful of triggers), leaving some use cases unattended. If you have some long-runnning job, you are stuck with HTTP requests with long timeouts and that's it.
I really hope this gets addressed in the future, will simplify things a lot for smaller businesses/solo projects. For example, at my company, we decided to move large parts of our infrastructure to Kubernetes (hosted at GCP). The lack of an elegant solution for background jobs in Cloud Run was the major reason for this decision, otherwise we would have just continued using it for the time to come.