That's a big question :). I don't think they're mutually exclusive. GKE provides more flexibility but requires more configuration. GAE is less flexible but more "serverless". GKE is probably more expensive for a single app, so I'd probably pick GAE for a single app. For a _project_, I'd have to understand more about what I'm building and what I need.

I'd also probably use Cloud Run over GAE, but that's a personal preference because I've been working closely with that product lately.