Often, there's not only a single way to look at one: There's a user interaction flow through components, but those components also consist of hardware; the hardware might be virtual and composed of several, spread, sub-components, or even containers. You can go down this path pretty deep, and arrive at several different representations of the system that are either impossible to visualise at the same time, or make it incomprehensible.
Ideally, I would want to have a way to document different facets of the system individually, but linked to each other, and be able to change my perspective at anytime. This would allow to flip between UX, network traffic, firewall boundaries, program flow, logical RPC flow, and so on; all while being able to view connected components for a given component at anytime. For example, inspecting an application, then viewing its network ports, then its runtime container, the hypervisor the container runs on, the cloud provider that sits in, and so on.
My idea so far is a graph database that contains all components and the edges between them. The tool would have to be as extensible as possible, so using something like HCL to describe the graph would be great, with extensions for all kinds of components and edges. And finally a viewer to render visual representations of one or more composable layers to flick through, and export etc.
I never got around to working on it yet, but if anyone else had the same idea, I'd be open to collaborating :)