I think I see what you're getting at - you're trying to create a standard way to build and deploy applications, in the way that Terraform is a standard way to build and deploy infrastructure, so to speak.
However, I think that one of the big differences here is that a lot of the reason why infrastructure scripts are messy is because they have to deal with state that's hidden behind a remote API, and that Terraform took the imperative APIs for providers like AWS and abstracted them behind a declarative configuration model that also kept track of state. So this was a huge value add compared to infrastructure scripts that would often get corner-cases involved with state wrong.
I'm not sure how much that's the case with application development though. Dockerfiles are declarative, as are Kubernetes manifests. The state of the environment is less of an issue - if a new version is being built, that's what gets deployed, and it overwrites what previously exists.
If there's any state management around application deployment, it's around detecting errors and rolling back if there are any. If Waypoint would move in the direction of standardizing that, so that developers could encode smoke tests for their application that Waypoint is constantly checking, then that would be huge - but it doesn't seem to be on your roadmap?