The title feels clickbaity. Direct API, CLI and MCP all have their uses.

Direct access (Curl/own small function): This requires agent to have full understanding of the API spec. Yes, context can be protected using progressive disclosure, but this essentially means agent needing to understand the API again and again, before every use. Also, a typical API spec may or may not be agent-friendly. If there are nuances when calling an endpoint, where do we put these? Into OAS description? Works, but clunky.

CLI: It works beautifully, especially when a 3rd party CLI already exists for a complex backend. Assumes a well documented, agent friendly CLI, most CLIs are designed for human or CI/CD consumption. Talking about MCP taking up too much context, think about agent starting with my_cli --help, and going down through the switches and parameters one at a time to figure out how the CLI should be called. Less of a problem when calling a well know CLI (e.g. aws), but anything more niche (or custom) requires multiple turns to compose the final CLI command.

MCP: Has its issues, but offers an agent-native solution. Everything agent needs to know about a tool becomes available at once. In an enterprise environment MCPs can be served through an MCP Gateway, providing governance and permission management, this is quite contrast against running a CLI that requires agent to have execute permissions in its shell.