If it's just an organizational comment then we can do that today, but I'm not really seeing what you're describing so I don't know.
My first reaction is that changing the way we organize stuff will not make it less messy, we will just move the mess around in different shapes.
What I really think is missing is a good documentation page that distills the knowledge required for writing Nostr apps. It would have to be something that doesn't follow the NIPs closely, but just lays a meaningful story on top of them and other real-world experience.